Invalid argument: --no-solvation
Usage: /nfs/home/rstein/zzz.github/DOCK/ligand/generate/build_database_ligand.sh [OPTIONS] <SOURCE_FILE>

  Options:
    -h, --help - Display this message and exit
    -H, --pH <PH_LEVELS> - 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 <NAME> - Override database name 
    -d, --dir <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 <BAD_CHARGE_FILE> - 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/7769621/working'
mkdir: created directory `/scratch/stefan/7769621/working/protonate'
Storing results in /scratch/stefan/7769621/finished
Working in /scratch/stefan/7769621/working
/scratch/stefan/7769621/working /scratch/stefan/7769621

/scratch/stefan/7769621/working/protonate /scratch/stefan/7769621/working /scratch/stefan/7769621
Precomputing protomers for all compounds (pH: 7.4)
/nfs/soft/jchem/jchem-19.15/bin/cxcalc: line 38: /nfs/home/stefan/.install4j: No such file or directory
/nfs/soft/jchem/jchem-19.15/bin/cxcalc: line 39: 7: Bad file descriptor
Nov 27, 2019 6:16:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:16:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:16:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:16:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:16:58 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:16:58 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:16:58 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:16:58 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:17:11 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:17:11 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:17:11 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:17:11 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:17:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:17:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:17:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:17:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:17:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:17:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:17:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:18:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:18:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:18:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:18:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:18:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:18:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:19:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:19:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:19:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:19:28 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:28 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:28 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:28 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:28 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:30 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:30 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:30 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:30 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:30 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 6:19:31 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:19:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:19:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:19:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:20:24 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:24 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:24 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:20:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:20:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:20:47 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:47 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:47 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:47 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:47 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:48 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:48 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:48 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:48 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:48 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:20:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:21:06 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:06 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:06 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:06 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:23 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:23 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:23 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:23 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:23 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:23 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:23 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:23 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:23 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:21:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:21:24 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:24 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:24 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:24 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:24 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:24 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:24 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:24 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:21:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:21:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:22:07 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:07 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:07 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:07 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:07 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:07 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:07 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:07 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:07 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:07 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:07 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:07 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:07 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:07 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:07 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:07 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:22 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:22 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:22 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:22 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:22 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:22 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:22 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:22 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:22 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:22:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:22:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:22:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:22:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:23:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:23:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:24:17 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
ph 7.4: 1153 protomers created
Coalesing and merging protomers
1136 protomers generated for 1000 compounds
Checking for new stereocenters and expanding
1136 protomers after new stereo-center expansion
/scratch/stefan/7769621/working /scratch/stefan/7769621

Bulk generating 3D conformations all protomers in /scratch/stefan/7769621/working/3D
mkdir: created directory `/scratch/stefan/7769621/working/3D'
We are using corina for 3D embeding
debuging info:: /scratch/stefan/7769621/working/protonate/xaaaabo-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'
1137 3D conformations generated for 1000 compounds

Building REAL300000040001
mkdir: created directory `/scratch/stefan/7769621/working/building'
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040001'
/scratch/stefan/7769621/working/building/REAL300000040001 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040001

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040001/0 /scratch/stefan/7769621/working/building/REAL300000040001 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1
`/scratch/stefan/7769621/working/3D/1' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2C=CSC2=CC=N1)C1=CC(C(=O)[O-])=CC=C1O)

`REAL300000040001.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040001.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040001/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040001 none CC(=NNC1=C2C=CSC2=CC=N1)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 50, 74, 74, 74, 74, 74, 74, 74, 74, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 11, 11, 11, 50, 74, 74, 74, 74, 1, 1, 1, 2] 148
rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 165
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040001 none CC(=NNC1=C2C=CSC2=CC=N1)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [31, 32, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 74, 74, 74, 74, 74, 74, 74, 74, 74, 32, 32, 32, 9, 1, 1, 1, 1, 74, 74, 74, 148] 148
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 34, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 267
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040001 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040001
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `/scratch/stefan/7769621/finished'
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040001/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040001
Building REAL300000040002
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040002'
/scratch/stefan/7769621/working/building/REAL300000040002 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040002

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040002/0 /scratch/stefan/7769621/working/building/REAL300000040002 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 2)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/2
`/scratch/stefan/7769621/working/3D/2' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC1=C2C=CSC2=CC=N1)C1=CC(C(=O)[O-])=CC=C1F)

`REAL300000040002.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040002.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040002/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040002 none CCC(=NNC1=C2C=CSC2=CC=N1)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 14, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 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, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 12, 1, 12, 12, 76, 185, 185, 185, 185, 185, 185, 185, 185, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 76, 185, 185, 185, 185, 1, 1, 1] 201
rigid atoms, others: [2, 35, 36, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 455
number of broken/clashed sets: 61
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040002 none CCC(=NNC1=C2C=CSC2=CC=N1)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 14, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 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, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [115, 51, 52, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 185, 185, 185, 185, 185, 185, 185, 185, 185, 115, 115, 115, 115, 115, 11, 1, 1, 1, 1, 185, 185, 185] 201
rigid atoms, others: [32, 33, 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, 34, 35, 36])
total number of confs: 567
number of broken/clashed sets: 61
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040002 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040002/1 /scratch/stefan/7769621/working/building/REAL300000040002 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 3)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/3
`/scratch/stefan/7769621/working/3D/3' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(N=NC1=C2C=CSC2=CC=N1)C1=CC(C(=O)[O-])=CC=C1F)

`REAL300000040002.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040002.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040002/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040002 none CCC(N=NC1=C2C=CSC2=CC=N1)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 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, 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
158  conformations in input
total number of sets (complete confs): 158
using faster count positions algorithm for large data
unique positions, atoms: [17, 11, 1, 11, 60, 60, 158, 158, 158, 158, 158, 158, 158, 158, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 20, 20, 20, 20, 20, 11, 158, 158, 158, 158, 1, 1, 1] 158
rigid atoms, others: [2, 35, 36, 34, 14, 15, 16, 17, 20, 21, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 298
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040002 none CCC(N=NC1=C2C=CSC2=CC=N1)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 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, 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
158  conformations in input
total number of sets (complete confs): 158
using faster count positions algorithm for large data
unique positions, atoms: [72, 54, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 158, 158, 158, 158, 158, 158, 158, 158, 158, 81, 81, 81, 81, 81, 54, 1, 1, 1, 1, 158, 158, 158] 158
rigid atoms, others: [32, 33, 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, 34, 35, 36])
total number of confs: 512
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040002 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040002
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040002/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040002/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040002
Building REAL300000040003
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040003'
/scratch/stefan/7769621/working/building/REAL300000040003 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040003

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040003/0 /scratch/stefan/7769621/working/building/REAL300000040003 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 4)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/4
`/scratch/stefan/7769621/working/3D/4' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=NNC(C=NNC3=C4C=CSC4=CC=N3)=C2C=C1)

`REAL300000040003.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040003.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040003/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040003 none O=C([O-])C1=CC2=NNC(C=NNC3=C4C=CSC4=CC=N3)=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [47, 47, 47, 47, 47, 47, 47, 47, 38, 38, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 47, 47, 47, 47, 38, 12, 1, 1, 1, 1, 47, 47] 47
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 33, 32, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 78
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040003 none O=C([O-])C1=CC2=NNC(C=NNC3=C4C=CSC4=CC=N3)=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 28, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 8, 27, 47, 47, 47, 47, 1, 1] 47
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 21, 22, 23, 24, 25, 33] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31])
total number of confs: 95
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040003 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040003/1 /scratch/stefan/7769621/working/building/REAL300000040003 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 5)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/5
`/scratch/stefan/7769621/working/3D/5' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(C=NNC3=C4C=CSC4=CC=N3)=NNC2=C1)

`REAL300000040003.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040003.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040003/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040003 none O=C([O-])C1=CC=C2C(C=NNC3=C4C=CSC4=CC=N3)=NNC2=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [99, 99, 99, 99, 99, 99, 99, 59, 59, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 98, 99, 99, 99, 99, 99, 59, 12, 1, 1, 1, 1, 98, 99] 99
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 33, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 148
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040003 none O=C([O-])C1=CC=C2C(C=NNC3=C4C=CSC4=CC=N3)=NNC2=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 63, 99, 98, 99, 99, 99, 99, 99, 99, 1, 1, 1, 1, 1, 1, 12, 63, 99, 99, 99, 99, 1, 1] 99
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 33] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31])
total number of confs: 220
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040003 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040003
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040003/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040003/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040003
Building REAL300000040004
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040004'
/scratch/stefan/7769621/working/building/REAL300000040004 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040004

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040004/0 /scratch/stefan/7769621/working/building/REAL300000040004 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 6)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/6
`/scratch/stefan/7769621/working/3D/6' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2C=CSC2=CC=N1)C1=CC=CC(C(=O)[O-])=C1)

`REAL300000040004.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040004.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040004/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040004 none CC(=NNC1=C2C=CSC2=CC=N1)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 14, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 11, 11, 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, 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
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 12, 12, 47, 78, 78, 78, 78, 78, 78, 78, 78, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 12, 12, 47, 78, 78, 78, 78, 1, 1, 1, 1] 78
rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 17, 18, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 177
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040004 none CC(=NNC1=C2C=CSC2=CC=N1)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 14, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 11, 11, 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, 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
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [42, 43, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 78, 78, 78, 78, 78, 78, 78, 78, 43, 43, 43, 12, 1, 1, 1, 1, 78, 78, 78, 78] 78
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([0, 1, 2, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31])
total number of confs: 131
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040004 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040004
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040004/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040004
Building REAL300000040005
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040005'
/scratch/stefan/7769621/working/building/REAL300000040005 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040005

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040005/0 /scratch/stefan/7769621/working/building/REAL300000040005 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 7)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/7
`/scratch/stefan/7769621/working/3D/7' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CN1C=C(CN=NC2=C3C=CSC3=CC=N2)N=N1)

`REAL300000040005.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040005.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040005/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040005 none O=C([O-])CN1C=C(CN=NC2=C3C=CSC3=CC=N2)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 8, 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, 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, 136, 136, 136, 37, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 136, 136, 201, 201, 136, 37, 37, 1, 1, 1, 1] 201
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25])
total number of confs: 607
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040005 none O=C([O-])CN1C=C(CN=NC2=C3C=CSC3=CC=N2)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 8, 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, 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: [12, 6, 12, 1, 1, 1, 1, 1, 9, 70, 70, 136, 136, 136, 136, 136, 136, 136, 136, 1, 1, 6, 6, 1, 9, 9, 136, 136, 136, 136] 201
rigid atoms, others: [3, 4, 5, 6, 7, 19, 20, 23] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 24, 25, 26, 27, 28, 29])
total number of confs: 247
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040005 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040005/1 /scratch/stefan/7769621/working/building/REAL300000040005 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 8)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/8
`/scratch/stefan/7769621/working/3D/8' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CN1C=C(C=NNC2=C3C=CSC3=CC=N2)N=N1)

`REAL300000040005.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040005.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040005/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040005 none O=C([O-])CN1C=C(C=NNC2=C3C=CSC3=CC=N2)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [106, 106, 106, 64, 64, 64, 42, 42, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 64, 64, 106, 106, 64, 42, 10, 1, 1, 1, 1] 106
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25])
total number of confs: 298
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040005 none O=C([O-])CN1C=C(C=NNC2=C3C=CSC3=CC=N2)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [20, 8, 20, 1, 1, 1, 1, 1, 7, 7, 29, 64, 64, 64, 64, 64, 64, 64, 64, 1, 1, 8, 8, 1, 7, 29, 64, 64, 64, 64] 106
rigid atoms, others: [3, 4, 5, 6, 7, 19, 20, 23] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 24, 25, 26, 27, 28, 29])
total number of confs: 180
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040005 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040005
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040005/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040005/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040005
Building REAL300000040006
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040006'
/scratch/stefan/7769621/working/building/REAL300000040006 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040006

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040006/0 /scratch/stefan/7769621/working/building/REAL300000040006 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 9)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/9
`/scratch/stefan/7769621/working/3D/9' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2C=CSC2=CC=N1)C1=CC=C(C(=O)[O-])C(F)=C1)

`REAL300000040006.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040006.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040006/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040006 none CC(=NNC1=C2C=CSC2=CC=N1)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 14, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 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
135  conformations in input
total number of sets (complete confs): 135
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 12, 12, 59, 135, 135, 135, 135, 135, 135, 135, 135, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 12, 12, 12, 59, 135, 135, 135, 135, 1, 1, 1] 135
rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 17, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 260
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040006 none CC(=NNC1=C2C=CSC2=CC=N1)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 14, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 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, 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
135  conformations in input
total number of sets (complete confs): 135
using faster count positions algorithm for large data
unique positions, atoms: [53, 53, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 135, 135, 135, 135, 135, 135, 135, 135, 135, 54, 54, 54, 12, 1, 1, 1, 1, 135, 135, 135] 135
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 203
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040006 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040006
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040006/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040006
Building REAL300000040007
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040007'
/scratch/stefan/7769621/working/building/REAL300000040007 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040007

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040007/0 /scratch/stefan/7769621/working/building/REAL300000040007 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 10)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/10
`/scratch/stefan/7769621/working/3D/10' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CSC(C=NNC2=C3C=CSC3=CC=N2)=C1)

`REAL300000040007.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040007.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040007/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040007 none O=C([O-])C1=CSC(C=NNC2=C3C=CSC3=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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]
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, 47, 47, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 68, 68, 47, 13, 1, 1, 1, 1, 68] 68
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 27])
total number of confs: 113
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040007 none O=C([O-])C1=CSC(C=NNC2=C3C=CSC3=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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]
0  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 34, 68, 68, 68, 68, 68, 67, 68, 68, 1, 1, 8, 34, 68, 68, 67, 68, 1] 68
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26])
total number of confs: 139
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040007 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040007
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040007/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040007
Building REAL300000040008
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040008'
/scratch/stefan/7769621/working/building/REAL300000040008 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040008

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040008/0 /scratch/stefan/7769621/working/building/REAL300000040008 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 11)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/11
`/scratch/stefan/7769621/working/3D/11' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=C3C=CSC3=CC=N2)=CC=C1OCCC(=O)[O-])

`REAL300000040008.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040008.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040008/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040008 none COC1=CC(C=NNC2=C3C=CSC3=CC=N2)=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.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [75, 44, 44, 44, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 127, 190, 190, 201, 191, 75, 75, 75, 44, 16, 6, 1, 1, 1, 1, 44, 44, 190, 190, 190, 190] 201
rigid atoms, others: [32, 33, 34, 35, 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, 36, 37, 38, 39, 40, 41])
total number of confs: 601
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040008 none COC1=CC(C=NNC2=C3C=CSC3=CC=N2)=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.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [3, 1, 1, 1, 1, 1, 7, 7, 19, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 9, 21, 21, 33, 31, 3, 3, 3, 1, 7, 19, 43, 44, 44, 44, 1, 1, 21, 21, 21, 21] 201
rigid atoms, others: [1, 2, 3, 4, 5, 17, 18, 19, 20, 36, 29, 37] 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, 35, 38, 39, 40, 41])
total number of confs: 199
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040008 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040008/1 /scratch/stefan/7769621/working/building/REAL300000040008 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 12)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/12
`/scratch/stefan/7769621/working/3D/12' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(CN=NC2=C3C=CSC3=CC=N2)=CC=C1OCCC(=O)[O-])

`REAL300000040008.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040008.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040008/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040008 none COC1=CC(CN=NC2=C3C=CSC3=CC=N2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [107, 56, 56, 56, 14, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 166, 189, 189, 201, 199, 107, 107, 107, 56, 14, 14, 1, 1, 1, 1, 56, 56, 189, 189, 189, 189] 201
rigid atoms, others: [32, 33, 34, 35, 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, 36, 37, 38, 39, 40, 41])
total number of confs: 539
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040008 none COC1=CC(CN=NC2=C3C=CSC3=CC=N2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [3, 1, 1, 1, 1, 1, 6, 52, 52, 56, 56, 56, 56, 56, 56, 56, 56, 1, 1, 1, 1, 5, 9, 9, 17, 15, 3, 3, 3, 1, 6, 6, 56, 56, 56, 56, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [1, 2, 3, 4, 5, 17, 18, 19, 20, 36, 29, 37] 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, 35, 38, 39, 40, 41])
total number of confs: 133
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040008 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040008
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040008/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040008/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040008
Building REAL300000040009
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040009'
/scratch/stefan/7769621/working/building/REAL300000040009 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040009

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040009/0 /scratch/stefan/7769621/working/building/REAL300000040009 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 13)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/13
`/scratch/stefan/7769621/working/3D/13' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC2=C3C=CSC3=CC=N2)C(Cl)=C1)

`REAL300000040009.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040009.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040009/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040009 none O=C([O-])C1=CC=C(C=NNC2=C3C=CSC3=CC=N2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [40, 40, 40, 40, 40, 40, 35, 34, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 34, 12, 1, 1, 1, 1, 40] 40
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 30])
total number of confs: 68
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040009 none O=C([O-])C1=CC=C(C=NNC2=C3C=CSC3=CC=N2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 26, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 10, 26, 40, 40, 40, 40, 1] 40
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29])
total number of confs: 86
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040009 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040009
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040009/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040009
Building REAL300000040010
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040010'
/scratch/stefan/7769621/working/building/REAL300000040010 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040010

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040010/0 /scratch/stefan/7769621/working/building/REAL300000040010 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 14)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/14
`/scratch/stefan/7769621/working/3D/14' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2C=CSC2=CC=N1)C1=CC(C(=O)[O-])=C(C)N=C1C)

`REAL300000040010.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040010.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040010/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040010 none CC(=NNC1=C2C=CSC2=CC=N1)C1=CC(C(=O)[O-])=C(C)N=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.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, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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]
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: [9, 1, 9, 9, 57, 127, 127, 127, 127, 127, 127, 127, 127, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 9, 9, 9, 57, 127, 127, 127, 127, 1, 2, 2, 2, 2, 2, 2] 127
rigid atoms, others: [32, 1, 13, 14, 15, 16, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38])
total number of confs: 253
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040010 none CC(=NNC1=C2C=CSC2=CC=N1)C1=CC(C(=O)[O-])=C(C)N=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.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, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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]
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: [57, 58, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 58, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 58, 58, 58, 13, 1, 1, 1, 1, 127, 127, 127, 127, 127, 127, 127] 127
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 202
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040010 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040010
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040010/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040010
Building REAL300000040011
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040011'
/scratch/stefan/7769621/working/building/REAL300000040011 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040011

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040011/0 /scratch/stefan/7769621/working/building/REAL300000040011 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 15)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/15
`/scratch/stefan/7769621/working/3D/15' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C=NNC2=C3C=CSC3=CC=N2)=CC=C1O)

`REAL300000040011.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040011.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040011/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040011 none O=C([O-])C1=CC(C=NNC2=C3C=CSC3=CC=N2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 14, 1, 1, 1, 8, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [72, 72, 72, 72, 71, 40, 40, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 71, 40, 12, 1, 1, 1, 1, 72, 72, 144] 144
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31])
total number of confs: 253
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040011 none O=C([O-])C1=CC(C=NNC2=C3C=CSC3=CC=N2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 14, 1, 1, 1, 8, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 10, 38, 71, 71, 72, 71, 71, 71, 71, 71, 1, 1, 1, 1, 1, 10, 38, 72, 72, 71, 71, 1, 1, 2] 144
rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 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/7769621/working/building/REAL300000040011 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040011
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040011/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040011
Building REAL300000040012
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040012'
/scratch/stefan/7769621/working/building/REAL300000040012 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040012

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040012/0 /scratch/stefan/7769621/working/building/REAL300000040012 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 16)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/16
`/scratch/stefan/7769621/working/3D/16' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2C=CSC2=CC=N1)C1=CC(C(=O)[O-])=CC=C1C)

`REAL300000040012.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040012.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040012/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040012 none CC(=NNC1=C2C=CSC2=CC=N1)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 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, 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: [9, 1, 9, 9, 44, 73, 73, 73, 73, 73, 73, 73, 73, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 9, 9, 44, 73, 73, 73, 73, 1, 1, 1, 2, 2, 2] 73
rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36])
total number of confs: 161
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040012 none CC(=NNC1=C2C=CSC2=CC=N1)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 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, 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: [44, 45, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 73, 73, 73, 73, 73, 73, 73, 73, 73, 45, 45, 45, 13, 1, 1, 1, 1, 73, 73, 73, 73, 73, 73] 73
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36])
total number of confs: 122
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040012 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040012
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040012/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040012
Building REAL300000040013
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040013'
/scratch/stefan/7769621/working/building/REAL300000040013 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040013

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040013/0 /scratch/stefan/7769621/working/building/REAL300000040013 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 17)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/17
`/scratch/stefan/7769621/working/3D/17' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=C2C=CSC2=CC=N1)C1=CC=C(C(=O)[O-])O1)

`REAL300000040013.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040013.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040013/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040013 none CC(N=NC1=C2C=CSC2=CC=N1)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 12, 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, 2, 2, 3, 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: [13, 1, 13, 77, 77, 112, 112, 112, 112, 112, 112, 112, 112, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 112, 112, 112, 112, 1, 1] 112
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 181
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040013 none CC(N=NC1=C2C=CSC2=CC=N1)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 12, 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, 2, 2, 3, 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: [46, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 112, 112, 112, 112, 112, 112, 112, 46, 46, 46, 46, 1, 1, 1, 1, 112, 112] 112
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30])
total number of confs: 238
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040013 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040013/1 /scratch/stefan/7769621/working/building/REAL300000040013 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 18)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/18
`/scratch/stefan/7769621/working/3D/18' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2C=CSC2=CC=N1)C1=CC=C(C(=O)[O-])O1)

`REAL300000040013.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040013.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040013/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040013 none CC(=NNC1=C2C=CSC2=CC=N1)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 12, 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, 7, 7, 7, 7, 7, 2, 2, 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: [13, 1, 13, 13, 27, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 27, 38, 39, 39, 39, 1, 1] 39
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 87
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040013 none CC(=NNC1=C2C=CSC2=CC=N1)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 12, 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, 7, 7, 7, 7, 7, 2, 2, 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: [30, 30, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 39, 39, 39, 39, 39, 39, 39, 31, 31, 31, 12, 1, 1, 1, 1, 39, 39] 39
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30])
total number of confs: 74
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040013 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040013
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040013/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040013/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040013
Building REAL300000040014
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040014'
/scratch/stefan/7769621/working/building/REAL300000040014 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040014

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040014/0 /scratch/stefan/7769621/working/building/REAL300000040014 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 19)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/19
`/scratch/stefan/7769621/working/3D/19' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=C(C=NNC2=C3C=CSC3=CC=N2)C=C1)C(=O)[O-])

`REAL300000040014.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040014.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040014/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040014 none CC(OC1=CC=C(C=NNC2=C3C=CSC3=CC=N2)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.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.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, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 11, 11, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 155, 62, 36, 88, 88, 36, 36, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 88, 88, 201, 201, 201, 201, 201, 201, 201, 88, 88, 36, 9, 1, 1, 1, 1, 88, 88] 201
rigid atoms, others: [32, 33, 34, 35, 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, 36, 37])
total number of confs: 692
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040014 none CC(OC1=CC=C(C=NNC2=C3C=CSC3=CC=N2)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.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.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, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 11, 11, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 6, 1, 1, 1, 1, 1, 1, 7, 7, 36, 88, 88, 88, 88, 88, 87, 88, 88, 1, 1, 15, 22, 22, 15, 15, 15, 15, 1, 1, 7, 36, 88, 88, 87, 88, 1, 1] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 19, 20, 36, 28, 29, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35])
total number of confs: 233
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040014 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040014/1 /scratch/stefan/7769621/working/building/REAL300000040014 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 20)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/20
`/scratch/stefan/7769621/working/3D/20' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=C(CN=NC2=C3C=CSC3=CC=N2)C=C1)C(=O)[O-])

`REAL300000040014.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040014.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040014/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040014 none CC(OC1=CC=C(CN=NC2=C3C=CSC3=CC=N2)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.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, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 166, 76, 26, 77, 77, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 77, 77, 201, 201, 201, 201, 201, 201, 201, 77, 77, 21, 21, 1, 1, 1, 1, 77, 77] 201
rigid atoms, others: [32, 33, 34, 35, 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, 36, 37])
total number of confs: 627
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040014 none CC(OC1=CC=C(CN=NC2=C3C=CSC3=CC=N2)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.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, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 6, 1, 1, 1, 1, 1, 1, 8, 61, 61, 77, 77, 77, 77, 77, 77, 77, 77, 1, 1, 13, 18, 18, 13, 13, 13, 13, 1, 1, 8, 8, 77, 77, 77, 77, 1, 1] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 19, 20, 36, 28, 29, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35])
total number of confs: 173
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040014 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040014
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040014/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040014/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040014
Building REAL300000040015
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040015'
/scratch/stefan/7769621/working/building/REAL300000040015 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040015

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040015/0 /scratch/stefan/7769621/working/building/REAL300000040015 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 21)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/21
`/scratch/stefan/7769621/working/3D/21' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1CCC(N=NC2=C3C=CSC3=CC=N2)C2=CC=CC=C21)

`REAL300000040015.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040015.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040015/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040015 none O=C([O-])C1CCC(N=NC2=C3C=CSC3=CC=N2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.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: [11, 1, 11, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [19, 19, 19, 19, 19, 19, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 19, 19, 19, 19] 19
rigid atoms, others: [32, 33, 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, 34, 35, 36, 37])
total number of confs: 43
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040015 none O=C([O-])C1CCC(N=NC2=C3C=CSC3=CC=N2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.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: [11, 1, 11, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 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, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 1, 1, 1, 1] 19
rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37] set([0, 32, 2, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31])
total number of confs: 29
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040015 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040015/1 /scratch/stefan/7769621/working/building/REAL300000040015 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 22)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/22
`/scratch/stefan/7769621/working/3D/22' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1CCC(=NNC2=C3C=CSC3=CC=N2)C2=CC=CC=C21)

`REAL300000040015.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040015.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040015/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040015 none O=C([O-])C1CCC(=NNC2=C3C=CSC3=CC=N2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.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: [11, 1, 11, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 1, 1, 1, 1, 22, 22, 22, 22] 22
rigid atoms, others: [32, 33, 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, 34, 35, 36, 37])
total number of confs: 40
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040015 none O=C([O-])C1CCC(=NNC2=C3C=CSC3=CC=N2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.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: [11, 1, 11, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 22, 22, 22, 22, 1, 1, 1, 1] 22
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37] set([0, 32, 2, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31])
total number of confs: 43
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040015 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040015
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040015/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040015/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040015
Building REAL300000040016
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040016'
/scratch/stefan/7769621/working/building/REAL300000040016 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040016

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040016/0 /scratch/stefan/7769621/working/building/REAL300000040016 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 23)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/23
`/scratch/stefan/7769621/working/3D/23' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CN1C=C(CN=NC2=C3C=CSC3=CC=N2)C2=CC=CC=C21)

`REAL300000040016.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040016.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040016/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040016 none O=C([O-])CN1C=C(CN=NC2=C3C=CSC3=CC=N2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.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: [11, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 1, 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, 7, 7, 7, 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, 121, 121, 121, 35, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 121, 121, 121, 121, 121, 121, 201, 201, 121, 35, 35, 1, 1, 1, 1, 121, 121, 121, 121] 201
rigid atoms, others: [32, 33, 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, 34, 35, 36, 37])
total number of confs: 651
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040016 none O=C([O-])CN1C=C(CN=NC2=C3C=CSC3=CC=N2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.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: [11, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 8, 14, 1, 1, 1, 1, 1, 8, 65, 66, 121, 121, 121, 121, 121, 121, 121, 121, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 8, 121, 121, 121, 121, 1, 1, 1, 1] 201
rigid atoms, others: [35, 34, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 36, 27, 37] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 28, 29, 30, 31, 32, 33])
total number of confs: 235
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040016 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040016
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040016/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040016
Building REAL300000040017
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040017'
/scratch/stefan/7769621/working/building/REAL300000040017 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040017

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040017/0 /scratch/stefan/7769621/working/building/REAL300000040017 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 24)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/24
`/scratch/stefan/7769621/working/3D/24' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])C=C(C=NNC2=C3C=CSC3=CC=N2)N1)

`REAL300000040017.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040017.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040017/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040017 none CC1=C(C(=O)[O-])C=C(C=NNC2=C3C=CSC3=CC=N2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 73, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 73, 73, 73, 73, 73, 50, 13, 1, 1, 1, 1, 73] 73
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 112
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040017 none CC1=C(C(=O)[O-])C=C(C=NNC2=C3C=CSC3=CC=N2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 8, 8, 34, 73, 73, 73, 73, 73, 73, 73, 73, 1, 2, 2, 2, 1, 8, 34, 73, 73, 73, 73, 1] 73
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 20, 24, 31] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30])
total number of confs: 152
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040017 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040017/1 /scratch/stefan/7769621/working/building/REAL300000040017 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 25)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/25
`/scratch/stefan/7769621/working/3D/25' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])C=C(CN=NC2=C3C=CSC3=CC=N2)N1)

`REAL300000040017.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040017.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040017/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040017 none CC1=C(C(=O)[O-])C=C(CN=NC2=C3C=CSC3=CC=N2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 54, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 54, 54, 1, 1, 1, 1, 201] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 365
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040017 none CC1=C(C(=O)[O-])C=C(CN=NC2=C3C=CSC3=CC=N2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 9, 83, 83, 201, 201, 201, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 9, 9, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 20, 24, 31] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 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
/scratch/stefan/7769621/working/building/REAL300000040017 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040017
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040017/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040017/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040017
Building REAL300000040018
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040018'
/scratch/stefan/7769621/working/building/REAL300000040018 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040018

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040018/0 /scratch/stefan/7769621/working/building/REAL300000040018 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 26)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/26
`/scratch/stefan/7769621/working/3D/26' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2C=CSC2=CC=N1)C1=CC=CC(OCCCC(=O)[O-])=C1)

`REAL300000040018.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040018.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040018/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040018 none CC(=NNC1=C2C=CSC2=CC=N1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [9, 1, 9, 9, 17, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 6, 18, 27, 39, 53, 53, 1, 9, 9, 9, 17, 31, 31, 31, 31, 1, 1, 1, 18, 18, 26, 26, 39, 39, 1] 201
rigid atoms, others: [1, 34, 35, 36, 43, 13, 14, 15, 16, 17, 18, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42])
total number of confs: 281
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040018 none CC(=NNC1=C2C=CSC2=CC=N1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 31, 31, 31, 31, 31, 98, 142, 159, 201, 201, 201, 31, 9, 9, 9, 4, 1, 1, 1, 1, 31, 31, 31, 142, 142, 159, 159, 201, 201, 31] 201
rigid atoms, others: [32, 33, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 699
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040018 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040018/1 /scratch/stefan/7769621/working/building/REAL300000040018 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 27)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/27
`/scratch/stefan/7769621/working/3D/27' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=C2C=CSC2=CC=N1)C1=CC=CC(OCCCC(=O)[O-])=C1)

`REAL300000040018.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040018.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040018/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040018 none CC(N=NC1=C2C=CSC2=CC=N1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [6, 1, 6, 23, 23, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 6, 14, 19, 32, 47, 47, 1, 6, 6, 6, 6, 25, 25, 25, 25, 1, 1, 1, 15, 15, 18, 18, 32, 32, 1] 201
rigid atoms, others: [1, 34, 35, 36, 43, 13, 14, 15, 16, 17, 18, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42])
total number of confs: 243
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040018 none CC(N=NC1=C2C=CSC2=CC=N1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [8, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 25, 25, 25, 25, 25, 106, 137, 140, 201, 201, 201, 25, 8, 8, 8, 8, 1, 1, 1, 1, 25, 25, 25, 137, 137, 140, 140, 201, 201, 25] 201
rigid atoms, others: [32, 33, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 669
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040018 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040018
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040018/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040018/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040018
Building REAL300000040019
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040019'
/scratch/stefan/7769621/working/building/REAL300000040019 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040019

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040019/0 /scratch/stefan/7769621/working/building/REAL300000040019 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 28)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/28
`/scratch/stefan/7769621/working/3D/28' -> `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=NC1=C2C=CSC2=CC=N1)

`REAL300000040019.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040019.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040019/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040019 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=C2C=CSC2=CC=N1 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.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 24, 48, 54, 54, 54, 54, 54, 176, 201, 201, 201, 201, 54, 54, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 51, 51, 53, 54, 54, 54, 201, 201, 201, 201, 54, 54, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 45, 46, 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, 41, 42])
total number of confs: 536
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040019 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=C2C=CSC2=CC=N1 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.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 2, 1, 1, 1, 1, 1, 1, 11, 25, 25, 34, 34, 1, 1, 7, 35, 35, 54, 54, 54, 54, 54, 54, 54, 54, 7, 7, 7, 7, 3, 3, 2, 2, 1, 1, 25, 25, 25, 25, 1, 1, 54, 54, 54, 54] 201
rigid atoms, others: [35, 4, 5, 6, 7, 8, 41, 42, 14, 15, 3, 36] 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, 33, 34, 37, 38, 39, 40, 43, 44, 45, 46])
total number of confs: 201
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040019 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040019
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040019/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040019
Building REAL300000040020
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040020'
/scratch/stefan/7769621/working/building/REAL300000040020 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040020

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040020/0 /scratch/stefan/7769621/working/building/REAL300000040020 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 29)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/29
`/scratch/stefan/7769621/working/3D/29' -> `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=NC1=C2C=CSC2=CC=N1)

`REAL300000040020.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040020.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040020/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040020 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=C2C=CSC2=CC=N1 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.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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, 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: [22, 5, 22, 48, 55, 55, 55, 55, 55, 144, 201, 201, 201, 55, 55, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 53, 53, 53, 55, 55, 55, 201, 201, 55, 55, 1, 1, 1, 1] 201
rigid atoms, others: [40, 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])
total number of confs: 649
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040020 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=C2C=CSC2=CC=N1 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.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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, 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: [9, 3, 2, 1, 1, 1, 1, 1, 1, 6, 19, 29, 29, 1, 1, 9, 40, 40, 55, 55, 55, 55, 55, 55, 55, 55, 9, 9, 9, 9, 3, 3, 2, 2, 1, 1, 19, 19, 1, 1, 55, 55, 55, 55] 201
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 39, 13, 14, 35, 38] 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, 32, 33, 36, 37, 40, 41, 42, 43])
total number of confs: 189
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040020 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040020
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040020/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040020
Building REAL300000040021
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040021'
/scratch/stefan/7769621/working/building/REAL300000040021 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040021

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040021/0 /scratch/stefan/7769621/working/building/REAL300000040021 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 30)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/30
`/scratch/stefan/7769621/working/3D/30' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2C=CSC2=CC=N1)C1=CC=CC(OC(C)C(=O)[O-])=C1)

`REAL300000040021.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040021.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040021/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040021 none CC(=NNC1=C2C=CSC2=CC=N1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 26, 62, 62, 62, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 1, 10, 24, 24, 32, 32, 1, 11, 11, 11, 26, 62, 62, 62, 62, 1, 1, 1, 24, 24, 24, 24, 1] 201
rigid atoms, others: [1, 34, 35, 33, 40, 13, 14, 15, 16, 17, 18, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39])
total number of confs: 221
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040021 none CC(=NNC1=C2C=CSC2=CC=N1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 23, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 62, 62, 62, 62, 62, 171, 201, 201, 201, 201, 62, 24, 24, 24, 6, 1, 1, 1, 1, 62, 62, 62, 201, 201, 201, 201, 62] 201
rigid atoms, others: [32, 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, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 419
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040021 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040021/1 /scratch/stefan/7769621/working/building/REAL300000040021 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 31)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/31
`/scratch/stefan/7769621/working/3D/31' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=C2C=CSC2=CC=N1)C1=CC=CC(OC(C)C(=O)[O-])=C1)

`REAL300000040021.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040021.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040021/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040021 none CC(N=NC1=C2C=CSC2=CC=N1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 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, 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]
0  hydrogens 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, 34, 34, 52, 52, 52, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 1, 10, 26, 26, 34, 34, 1, 7, 7, 7, 7, 52, 52, 52, 52, 1, 1, 1, 26, 26, 26, 26, 1] 201
rigid atoms, others: [1, 34, 35, 33, 40, 13, 14, 15, 16, 17, 18, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39])
total number of confs: 196
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040021 none CC(N=NC1=C2C=CSC2=CC=N1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 52, 52, 52, 52, 52, 169, 201, 201, 201, 201, 52, 22, 22, 22, 22, 1, 1, 1, 1, 52, 52, 52, 201, 201, 201, 201, 52] 201
rigid atoms, others: [32, 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, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 454
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040021 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040021
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040021/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040021/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040021
Building REAL300000040022
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040022'
/scratch/stefan/7769621/working/building/REAL300000040022 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040022

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040022/0 /scratch/stefan/7769621/working/building/REAL300000040022 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 32)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/32
`/scratch/stefan/7769621/working/3D/32' -> `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=NC1=C2C=CSC2=CC=N1)

`REAL300000040022.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040022.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040022/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040022 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=C2C=CSC2=CC=N1 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.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 6, 25, 46, 51, 51, 51, 51, 51, 186, 201, 201, 201, 201, 51, 51, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 48, 48, 51, 51, 51, 51, 201, 201, 201, 201, 51, 51, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 45, 46, 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, 41, 42])
total number of confs: 462
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040022 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=C2C=CSC2=CC=N1 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.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 2, 1, 1, 1, 1, 1, 1, 6, 13, 13, 20, 20, 1, 1, 8, 36, 36, 51, 51, 51, 51, 51, 51, 51, 51, 8, 8, 8, 8, 3, 3, 2, 2, 1, 1, 13, 13, 13, 13, 1, 1, 51, 51, 51, 51] 201
rigid atoms, others: [35, 4, 5, 6, 7, 8, 41, 42, 14, 15, 3, 36] 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, 33, 34, 37, 38, 39, 40, 43, 44, 45, 46])
total number of confs: 156
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040022 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040022
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040022/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040022
Building REAL300000040023
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040023'
/scratch/stefan/7769621/working/building/REAL300000040023 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040023

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040023/0 /scratch/stefan/7769621/working/building/REAL300000040023 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 33)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/33
`/scratch/stefan/7769621/working/3D/33' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC1=C2C=CSC2=CC=N1)C1=CC=C(OCCCCC(=O)[O-])C=C1)

`REAL300000040023.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040023.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040023/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040023 none CCC(=NNC1=C2C=CSC2=CC=N1)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.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [10, 7, 1, 7, 7, 18, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 6, 9, 20, 20, 31, 35, 37, 1, 1, 10, 10, 10, 10, 10, 18, 33, 33, 33, 33, 1, 1, 9, 9, 20, 20, 20, 20, 30, 30, 1, 1] 201
rigid atoms, others: [48, 2, 49, 38, 39, 14, 15, 16, 17, 18, 26, 27] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 241
number of broken/clashed sets: 31
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040023 none CCC(=NNC1=C2C=CSC2=CC=N1)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.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [22, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 33, 33, 14, 14, 94, 116, 161, 161, 182, 194, 198, 33, 33, 22, 22, 22, 22, 22, 5, 1, 1, 1, 1, 33, 33, 116, 116, 161, 161, 161, 161, 182, 182, 33, 33] 201
rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 36, 37] set([0, 1, 2, 3, 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: 756
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040023 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040023/1 /scratch/stefan/7769621/working/building/REAL300000040023 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 34)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/34
`/scratch/stefan/7769621/working/3D/34' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(N=NC1=C2C=CSC2=CC=N1)C1=CC=C(OCCCCC(=O)[O-])C=C1)

`REAL300000040023.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040023.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040023/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040023 none CCC(N=NC1=C2C=CSC2=CC=N1)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 4, 1, 4, 13, 13, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 6, 11, 24, 28, 46, 51, 54, 1, 1, 5, 5, 5, 5, 5, 4, 17, 17, 17, 17, 1, 1, 11, 11, 24, 24, 28, 28, 45, 45, 1, 1] 201
rigid atoms, others: [48, 2, 49, 38, 39, 14, 15, 16, 17, 18, 26, 27] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 267
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040023 none CCC(N=NC1=C2C=CSC2=CC=N1)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [15, 10, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 17, 17, 12, 12, 70, 80, 120, 130, 182, 195, 201, 17, 17, 15, 15, 15, 15, 15, 10, 1, 1, 1, 1, 17, 17, 80, 79, 120, 120, 130, 130, 182, 182, 17, 17] 201
rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 36, 37] set([0, 1, 2, 3, 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: 790
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040023 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040023
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040023/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040023/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040023
Building REAL300000040024
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040024'
/scratch/stefan/7769621/working/building/REAL300000040024 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040024

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040024/0 /scratch/stefan/7769621/working/building/REAL300000040024 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 35)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/35
`/scratch/stefan/7769621/working/3D/35' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2C=CSC2=CC=N1)C1=CSC(C(=O)[O-])=C1)

`REAL300000040024.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040024.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040024/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040024 none CC(=NNC1=C2C=CSC2=CC=N1)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 14, 1, 1, 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, 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
84  conformations in input
total number of sets (complete confs): 84
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 12, 12, 47, 84, 84, 84, 84, 84, 84, 84, 84, 1, 1, 1, 1, 1, 2, 2, 1, 12, 12, 12, 47, 84, 84, 84, 84, 1, 1] 84
rigid atoms, others: [1, 13, 14, 15, 16, 17, 20, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 183
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040024 none CC(=NNC1=C2C=CSC2=CC=N1)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 14, 1, 1, 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, 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
84  conformations in input
total number of sets (complete confs): 84
using faster count positions algorithm for large data
unique positions, atoms: [38, 39, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 84, 84, 84, 84, 84, 84, 84, 39, 39, 39, 12, 1, 1, 1, 1, 84, 84] 84
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30])
total number of confs: 135
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040024 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040024
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040024/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040024
Building REAL300000040025
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040025'
/scratch/stefan/7769621/working/building/REAL300000040025 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040025

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040025/0 /scratch/stefan/7769621/working/building/REAL300000040025 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 36)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/36
`/scratch/stefan/7769621/working/3D/36' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=C3C=CSC3=CC=N2)C1)

`REAL300000040025.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040025.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040025/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040025 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=C3C=CSC3=CC=N2)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.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', '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, 5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 5, 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]
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: [24, 24, 24, 24, 24, 27, 27, 27, 27, 27, 24, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 27, 27, 27, 27, 27, 24, 24, 24, 1, 1, 1, 1, 24, 24] 27
rigid atoms, others: [32, 33, 34, 35, 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, 36, 37])
total number of confs: 61
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: REAL300000040025 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=C3C=CSC3=CC=N2)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.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', '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, 5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 5, 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]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 27, 27, 27, 27, 27, 27, 27, 27, 5, 1, 1, 1, 1, 1, 5, 5, 5, 27, 27, 27, 27, 5, 5] 27
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 27, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 51
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040025 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=C3C=CSC3=CC=N2)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.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', '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, 5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 5, 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]
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: [3, 1, 3, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 1, 5, 5, 5, 5, 5, 1, 1, 1, 24, 24, 24, 24, 1, 1] 27
rigid atoms, others: [1, 3, 4, 37, 10, 11, 12, 23, 36, 29, 30, 31] set([0, 2, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 32, 33, 34, 35])
total number of confs: 42
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040025 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040025
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040025/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040025
Building REAL300000040026
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040026'
/scratch/stefan/7769621/working/building/REAL300000040026 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040026

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040026/0 /scratch/stefan/7769621/working/building/REAL300000040026 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 37)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/37
`/scratch/stefan/7769621/working/3D/37' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=C2C=CSC2=CC=N1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C)

`REAL300000040026.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040026.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040026/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040026 none CC(N=NC1=C2C=CSC2=CC=N1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 5, 7, 5, 5, 7, 5, 1, 11, 11, 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, 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]
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: [4, 1, 4, 23, 23, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 7, 13, 13, 1, 1, 1, 4, 4, 4, 4, 53, 53, 53, 53, 1, 1, 7, 7, 2, 2, 2, 2, 2, 2] 79
rigid atoms, others: [1, 34, 33, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 130
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040026 none CC(N=NC1=C2C=CSC2=CC=N1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 5, 7, 5, 5, 7, 5, 1, 11, 11, 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, 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]
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: [42, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 53, 53, 53, 53, 53, 79, 79, 79, 53, 53, 53, 42, 42, 42, 42, 1, 1, 1, 1, 53, 53, 79, 79, 53, 53, 53, 53, 53, 53] 79
rigid atoms, others: [32, 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 321
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040026 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040026
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040026/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040026
Building REAL300000040027
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040027'
/scratch/stefan/7769621/working/building/REAL300000040027 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040027

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040027/0 /scratch/stefan/7769621/working/building/REAL300000040027 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 38)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/38
`/scratch/stefan/7769621/working/3D/38' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCCCCCC(=O)[O-])N=NC1=C2C=CSC2=CC=N1)

`REAL300000040027.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040027.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040027/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040027 none CC(CCCCCCC(=O)[O-])N=NC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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, 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: [29, 6, 29, 57, 71, 81, 113, 125, 201, 201, 201, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 62, 62, 71, 68, 87, 87, 113, 109, 132, 132, 200, 199, 1, 1, 1, 1] 201
rigid atoms, others: [38, 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])
total number of confs: 1026
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040027 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040027
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040027/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040027
Building REAL300000040028
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040028'
/scratch/stefan/7769621/working/building/REAL300000040028 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040028

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040028/0 /scratch/stefan/7769621/working/building/REAL300000040028 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 39)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/39
`/scratch/stefan/7769621/working/3D/39' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(CC(=O)[O-])CCC1N=NC1=C2C=CSC2=CC=N1)

`REAL300000040028.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040028.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040028/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040028 none CC1C(CC(=O)[O-])CCC1N=NC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 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
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [39, 39, 39, 39, 66, 66, 66, 39, 39, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 37, 39, 66, 66, 39, 39, 39, 39, 39, 1, 1, 1, 1] 66
rigid atoms, others: [33, 34, 35, 36, 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])
total number of confs: 232
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040028 none CC1C(CC(=O)[O-])CCC1N=NC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 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
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 9, 13, 13, 1, 1, 1, 1, 12, 12, 39, 39, 39, 39, 39, 39, 39, 39, 2, 2, 2, 1, 1, 9, 9, 1, 1, 1, 1, 1, 39, 39, 39, 39] 66
rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 24, 25, 28, 29, 30, 31] set([4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 33, 34, 35, 36])
total number of confs: 97
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040028 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040028
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040028/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040028
Building REAL300000040029
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040029'
/scratch/stefan/7769621/working/building/REAL300000040029 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040029

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040029/0 /scratch/stefan/7769621/working/building/REAL300000040029 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 40)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/40
`/scratch/stefan/7769621/working/3D/40' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2C=CSC2=CC=N1)C1=CC(C(=O)[O-])=CS1)

`REAL300000040029.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040029.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040029/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040029 none CC(=NNC1=C2C=CSC2=CC=N1)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 1, 14, 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, 7, 7, 7, 7, 2, 2, 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: [12, 1, 12, 12, 58, 95, 95, 95, 95, 95, 94, 95, 95, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 58, 95, 95, 95, 95, 1, 1] 95
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 214
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040029 none CC(=NNC1=C2C=CSC2=CC=N1)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 1, 14, 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, 7, 7, 7, 7, 2, 2, 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, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 95, 95, 95, 95, 95, 95, 95, 50, 50, 50, 13, 1, 1, 1, 1, 95, 95] 95
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30])
total number of confs: 149
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040029 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040029/1 /scratch/stefan/7769621/working/building/REAL300000040029 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 41)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/41
`/scratch/stefan/7769621/working/3D/41' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=C2C=CSC2=CC=N1)C1=CC(C(=O)[O-])=CS1)

`REAL300000040029.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040029.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040029/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040029 none CC(N=NC1=C2C=CSC2=CC=N1)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 1, 14, 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, 2, 2, 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: [13, 1, 13, 85, 85, 115, 115, 115, 115, 115, 115, 115, 115, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 115, 115, 115, 115, 1, 1] 115
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 181
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040029 none CC(N=NC1=C2C=CSC2=CC=N1)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 1, 14, 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, 2, 2, 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: [46, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 115, 115, 115, 115, 115, 115, 115, 46, 46, 46, 46, 1, 1, 1, 1, 115, 115] 115
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30])
total number of confs: 245
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040029 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040029
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040029/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040029/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040029
Building REAL300000040030
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040030'
/scratch/stefan/7769621/working/building/REAL300000040030 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040030

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040030/0 /scratch/stefan/7769621/working/building/REAL300000040030 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 42)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/42
`/scratch/stefan/7769621/working/3D/42' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(N=NC2=C3C=CSC3=CC=N2)CCC(C(=O)[O-])C1(C)C)

`REAL300000040030.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040030.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040030/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040030 none CC1C(N=NC2=C3C=CSC3=CC=N2)CCC(C(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', '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, 14, 1, 1, 1, 8, 5, 5, 5, 1, 11, 11, 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: [7, 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]
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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 16
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30, 31] set([0, 1, 2, 3, 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])
total number of confs: 31
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040030 none CC1C(N=NC2=C3C=CSC3=CC=N2)CCC(C(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', '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, 14, 1, 1, 1, 8, 5, 5, 5, 1, 11, 11, 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: [7, 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]
0  hydrogens need rotated
16  conformations in input
total number of sets (complete confs): 16
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 10, 10, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 3, 3, 1, 1, 1, 2, 2, 2, 1, 1, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 16
rigid atoms, others: [0, 1, 2, 3, 36, 33, 38, 32, 39, 34, 14, 15, 16, 17, 35, 20, 21, 22, 26, 27, 37] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 23, 24, 25, 28, 29, 30, 31, 40, 41, 42])
total number of confs: 40
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040030 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040030
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040030/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040030
Building REAL300000040031
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040031'
/scratch/stefan/7769621/working/building/REAL300000040031 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040031

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040031/0 /scratch/stefan/7769621/working/building/REAL300000040031 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 43)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/43
`/scratch/stefan/7769621/working/3D/43' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(C(=O)[O-])CCC1N=NC1=C2C=CSC2=CC=N1)

`REAL300000040031.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040031.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040031/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040031 none CC1CC(C(=O)[O-])CCC1N=NC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 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
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1] 25
rigid atoms, others: [33, 34, 35, 36, 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])
total number of confs: 57
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040031 none CC1CC(C(=O)[O-])CCC1N=NC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 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
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 25
rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([33, 34, 35, 36, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23])
total number of confs: 43
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040031 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040031
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040031/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040031
Building REAL300000040032
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040032'
/scratch/stefan/7769621/working/building/REAL300000040032 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040032

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040032/0 /scratch/stefan/7769621/working/building/REAL300000040032 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 44)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/44
`/scratch/stefan/7769621/working/3D/44' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(N=NC2=C3C=CSC3=CC=N2)CCC1C(=O)[O-])

`REAL300000040032.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040032.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040032/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040032 none CC1CC(N=NC2=C3C=CSC3=CC=N2)CCC1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.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']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 5, 5, 5, 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, 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
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, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 11, 11, 11, 11, 11] 11
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36])
total number of confs: 26
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040032 none CC1CC(N=NC2=C3C=CSC3=CC=N2)CCC1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.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']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 5, 5, 5, 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, 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
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 1, 11, 11, 11, 11, 1, 1, 1, 1, 1] 11
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 15, 16, 17, 18, 35, 24, 25, 26, 27, 36] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 28, 29, 30, 31])
total number of confs: 25
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040032 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040032
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040032/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040032
Building REAL300000040033
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040033'
/scratch/stefan/7769621/working/building/REAL300000040033 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040033

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040033/0 /scratch/stefan/7769621/working/building/REAL300000040033 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 45)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/45
`/scratch/stefan/7769621/working/3D/45' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(C)=NNC2=C3C=CSC3=CC=N2)=CC=C1OCCCC(=O)[O-])

`REAL300000040033.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040033.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040033/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040033 none COC1=CC(C(C)=NNC2=C3C=CSC3=CC=N2)=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.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7]
0  hydrogens 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, 39, 39, 39, 13, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 100, 173, 176, 201, 201, 201, 67, 67, 67, 39, 13, 13, 13, 3, 1, 1, 1, 1, 39, 39, 173, 173, 176, 176, 201, 201] 201
rigid atoms, others: [36, 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, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 712
number of broken/clashed sets: 116
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040033 none COC1=CC(C(C)=NNC2=C3C=CSC3=CC=N2)=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.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7]
0  hydrogens 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, 25, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 7, 13, 15, 23, 27, 27, 3, 3, 3, 1, 7, 7, 7, 25, 39, 39, 39, 39, 1, 1, 13, 13, 15, 15, 23, 23] 201
rigid atoms, others: [1, 2, 3, 4, 5, 40, 41, 18, 19, 20, 21, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47])
total number of confs: 196
number of broken/clashed sets: 116
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040033 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040033/1 /scratch/stefan/7769621/working/building/REAL300000040033 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 46)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/46
`/scratch/stefan/7769621/working/3D/46' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(C)N=NC2=C3C=CSC3=CC=N2)=CC=C1OCCCC(=O)[O-])

`REAL300000040033.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040033.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040033/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040033 none COC1=CC(C(C)N=NC2=C3C=CSC3=CC=N2)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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]
0  hydrogens 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, 30, 30, 30, 10, 3, 10, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 97, 167, 169, 201, 201, 201, 54, 54, 54, 30, 10, 10, 10, 10, 1, 1, 1, 1, 30, 30, 167, 167, 169, 169, 201, 201] 201
rigid atoms, others: [36, 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, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 730
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040033 none COC1=CC(C(C)N=NC2=C3C=CSC3=CC=N2)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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]
0  hydrogens 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, 24, 24, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 6, 16, 17, 27, 36, 36, 3, 3, 3, 1, 6, 6, 6, 6, 30, 30, 30, 30, 1, 1, 16, 16, 17, 17, 27, 27] 201
rigid atoms, others: [1, 2, 3, 4, 5, 40, 41, 18, 19, 20, 21, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47])
total number of confs: 206
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040033 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040033
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040033/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040033/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040033
Building REAL300000040034
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040034'
/scratch/stefan/7769621/working/building/REAL300000040034 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040034

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040034/0 /scratch/stefan/7769621/working/building/REAL300000040034 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 47)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/47
`/scratch/stefan/7769621/working/3D/47' -> `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(N=NC2=C3C=CSC3=CC=N2)C1)

`REAL300000040034.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040034.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040034/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040034 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=C3C=CSC3=CC=N2)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', '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, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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, 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
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [24, 22, 24, 22, 22, 53, 53, 53, 53, 53, 53, 22, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 53, 53, 53, 53, 22, 22, 22, 1, 1, 1, 1, 22, 22] 53
rigid atoms, others: [32, 33, 34, 35, 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, 36, 37])
total number of confs: 109
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: REAL300000040034 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=C3C=CSC3=CC=N2)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', '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, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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, 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
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [16, 10, 16, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 29, 29, 53, 53, 53, 53, 53, 53, 53, 53, 10, 1, 1, 1, 1, 10, 10, 10, 53, 53, 53, 53, 10, 10] 53
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 108
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040034 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=C3C=CSC3=CC=N2)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', '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, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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, 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
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 10, 10, 10, 10, 10, 10, 1, 1, 1, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 1, 10, 10, 10, 10, 1, 1, 1, 22, 22, 22, 22, 1, 1] 53
rigid atoms, others: [1, 3, 4, 37, 11, 12, 13, 24, 36, 29, 30, 31] set([0, 2, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 32, 33, 34, 35])
total number of confs: 45
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040034 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040034
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040034/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040034
Building REAL300000040035
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040035'
/scratch/stefan/7769621/working/building/REAL300000040035 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040035

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040035/0 /scratch/stefan/7769621/working/building/REAL300000040035 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 48)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/48
`/scratch/stefan/7769621/working/3D/48' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC1=C2C=CSC2=CC=N1)

`REAL300000040035.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040035.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040035/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040035 none O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC1=C2C=CSC2=CC=N1 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', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 1, 1, 1, 1] 18
rigid atoms, others: [34, 35, 36, 37, 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])
total number of confs: 32
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040035 none O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC1=C2C=CSC2=CC=N1 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', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 18] 18
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32] set([33, 34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 22, 23])
total number of confs: 30
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040035 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040035/1 /scratch/stefan/7769621/working/building/REAL300000040035 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 49)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/49
`/scratch/stefan/7769621/working/3D/49' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(=C1)CCCC2N=NC1=C2C=CSC2=CC=N1)

`REAL300000040035.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040035.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040035/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040035 none O=C([O-])C1=CC=C2C(=C1)CCCC2N=NC1=C2C=CSC2=CC=N1 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', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1] 18
rigid atoms, others: [34, 35, 36, 37, 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])
total number of confs: 39
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040035 none O=C([O-])C1=CC=C2C(=C1)CCCC2N=NC1=C2C=CSC2=CC=N1 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', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18] 18
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33] set([0, 2, 35, 36, 37, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23])
total number of confs: 29
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040035 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040035
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040035/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040035/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040035
Building REAL300000040036
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040036'
/scratch/stefan/7769621/working/building/REAL300000040036 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040036

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040036/0 /scratch/stefan/7769621/working/building/REAL300000040036 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 50)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/50
`/scratch/stefan/7769621/working/3D/50' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1(C(=O)[O-])CCC1)N=NC1=C2C=CSC2=CC=N1)

`REAL300000040036.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040036.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040036/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040036 none CC(CC1(C(=O)[O-])CCC1)N=NC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 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
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [34, 8, 34, 43, 60, 60, 60, 60, 60, 60, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 43, 43, 60, 60, 60, 60, 60, 60, 1, 1, 1, 1] 60
rigid atoms, others: [33, 34, 35, 36, 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])
total number of confs: 218
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040036 none CC(CC1(C(=O)[O-])CCC1)N=NC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 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
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [10, 7, 1, 1, 1, 3, 3, 1, 1, 1, 10, 36, 36, 60, 60, 60, 60, 60, 60, 60, 60, 10, 10, 10, 10, 7, 7, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60] 60
rigid atoms, others: [32, 2, 3, 4, 7, 8, 9, 27, 28, 29, 30, 31] set([0, 1, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 33, 34, 35, 36])
total number of confs: 118
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040036 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040036
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040036/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040036
Building REAL300000040037
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040037'
/scratch/stefan/7769621/working/building/REAL300000040037 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040037

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040037/0 /scratch/stefan/7769621/working/building/REAL300000040037 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 51)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/51
`/scratch/stefan/7769621/working/3D/51' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C2C(=C1)OC(C(C)N=NC1=C3C=CSC3=CC=N1)=C2CC(=O)[O-])

`REAL300000040037.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040037.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040037/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040037 none CC1=CC=C2C(=C1)OC(C(C)N=NC1=C3C=CSC3=CC=N1)=C2CC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 5, 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, 3, 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]
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: [104, 104, 104, 104, 104, 104, 104, 104, 44, 7, 44, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 104, 104, 135, 135, 135, 104, 104, 104, 104, 104, 104, 44, 44, 44, 44, 1, 1, 1, 1, 135, 135] 135
rigid atoms, others: [37, 38, 39, 40, 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, 41, 42])
total number of confs: 416
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040037 none CC1=CC=C2C(=C1)OC(C(C)N=NC1=C3C=CSC3=CC=N1)=C2CC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 5, 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, 3, 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]
0  hydrogens need rotated
135  conformations in input
total number of sets (complete confs): 135
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 44, 44, 104, 104, 104, 104, 104, 104, 104, 104, 1, 1, 3, 7, 7, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 104, 104, 104, 104, 3, 3] 135
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 22, 23, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 180
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040037 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040037/1 /scratch/stefan/7769621/working/building/REAL300000040037 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 52)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/52
`/scratch/stefan/7769621/working/3D/52' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2C=CSC2=CC=N1)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1)

`REAL300000040037.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040037.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040037/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040037 none CC(=NNC1=C2C=CSC2=CC=N1)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.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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]
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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 49, 106, 106, 106, 106, 106, 106, 106, 106, 1, 1, 1, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 49, 106, 106, 106, 106, 2, 2, 1, 1, 2, 2, 2, 1] 114
rigid atoms, others: [1, 37, 38, 42, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41])
total number of confs: 226
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040037 none CC(=NNC1=C2C=CSC2=CC=N1)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.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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]
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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [49, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 106, 106, 114, 114, 114, 106, 106, 106, 106, 106, 106, 106, 106, 50, 50, 50, 13, 1, 1, 1, 1, 114, 114, 106, 106, 106, 106, 106, 106] 114
rigid atoms, others: [32, 33, 34, 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, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 219
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040037 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040037
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040037/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040037/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040037
Building REAL300000040038
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040038'
/scratch/stefan/7769621/working/building/REAL300000040038 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040038

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040038/0 /scratch/stefan/7769621/working/building/REAL300000040038 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 53)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/53
`/scratch/stefan/7769621/working/3D/53' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=C2C=CSC2=CC=N1)

`REAL300000040038.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040038.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040038/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040038 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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, 2, 2, 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, 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, 72, 72, 72, 72, 40, 40, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 72, 72, 72, 72, 40, 11, 1, 1, 1, 1] 72
rigid atoms, others: [33, 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])
total number of confs: 113
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040038 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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, 2, 2, 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, 7, 7, 7]
0  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 12, 12, 44, 72, 72, 72, 72, 72, 72, 72, 72, 2, 2, 2, 1, 2, 2, 2, 1, 12, 44, 72, 72, 72, 72] 72
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 26, 30] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36])
total number of confs: 173
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040038 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040038
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040038/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040038
Building REAL300000040039
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040039'
/scratch/stefan/7769621/working/building/REAL300000040039 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040039

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040039/0 /scratch/stefan/7769621/working/building/REAL300000040039 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 54)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/54
`/scratch/stefan/7769621/working/3D/54' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(C=NNC2=C3C=CSC3=CC=N2)=C1Cl)

`REAL300000040039.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040039.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040039/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040039 none O=C([O-])C1=CC=CC(C=NNC2=C3C=CSC3=CC=N2)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 38, 38, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 38, 12, 1, 1, 1, 1] 50
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 80
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040039 none O=C([O-])C1=CC=CC(C=NNC2=C3C=CSC3=CC=N2)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 26, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 8, 26, 50, 50, 50, 50] 50
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30])
total number of confs: 102
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040039 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040039
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040039/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040039
Building REAL300000040040
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040040'
/scratch/stefan/7769621/working/building/REAL300000040040 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040040

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040040/0 /scratch/stefan/7769621/working/building/REAL300000040040 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 55)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/55
`/scratch/stefan/7769621/working/3D/55' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC1=C2C=CSC2=CC=N1)

`REAL300000040040.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040040.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040040/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040040 none O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC1=C2C=CSC2=CC=N1 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', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [18, 18, 18, 17, 17, 17, 17, 17, 17, 17, 17, 18, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 17, 18, 18, 17, 17, 18, 18, 18, 17, 18, 9, 1, 1, 1, 1] 18
rigid atoms, others: [37, 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])
total number of confs: 47
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040040 none O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC1=C2C=CSC2=CC=N1 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', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 18, 18, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 18, 18, 17, 17] 18
rigid atoms, others: [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] set([36, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21, 22, 23, 24])
total number of confs: 35
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040040 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040040/1 /scratch/stefan/7769621/working/building/REAL300000040040 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 56)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/56
`/scratch/stefan/7769621/working/3D/56' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(=C1)CCCCC2N=NC1=C2C=CSC2=CC=N1)

`REAL300000040040.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040040.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040040/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040040 none O=C([O-])C1=CC=C2C(=C1)CCCCC2N=NC1=C2C=CSC2=CC=N1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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, 1, 1, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1] 9
rigid atoms, others: [37, 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])
total number of confs: 17
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040040 none O=C([O-])C1=CC=C2C(=C1)CCCCC2N=NC1=C2C=CSC2=CC=N1 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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, 1, 1, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9] 9
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 2, 37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24])
total number of confs: 17
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040040 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040040
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040040/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040040/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040040
Building REAL300000040041
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040041'
/scratch/stefan/7769621/working/building/REAL300000040041 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040041

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040041/0 /scratch/stefan/7769621/working/building/REAL300000040041 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 57)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/57
`/scratch/stefan/7769621/working/3D/57' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC(C(=O)[O-])=C1C=NNC1=C2C=CSC2=CC=N1)

`REAL300000040041.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040041.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040041/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040041 none CN1N=CC(C(=O)[O-])=C1C=NNC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 30, 30, 30, 30, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 12, 1, 1, 1, 1] 30
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26])
total number of confs: 50
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040041 none CN1N=CC(C(=O)[O-])=C1C=NNC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 4, 4, 18, 30, 30, 30, 30, 30, 30, 30, 30, 2, 2, 2, 1, 4, 18, 30, 30, 30, 30] 30
rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 24] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30])
total number of confs: 74
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040041 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040041
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040041/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040041
Building REAL300000040042
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040042'
/scratch/stefan/7769621/working/building/REAL300000040042 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040042

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040042/0 /scratch/stefan/7769621/working/building/REAL300000040042 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 58)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/58
`/scratch/stefan/7769621/working/3D/58' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC2=C3C=CSC3=CC=N2)C=C1F)

`REAL300000040042.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040042.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040042/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040042 none O=C([O-])C1=CC=C(C=NNC2=C3C=CSC3=CC=N2)C=C1F NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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, 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, 117, 117, 117, 117, 116, 56, 56, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 116, 56, 12, 1, 1, 1, 1, 117] 117
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 30])
total number of confs: 193
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040042 none O=C([O-])C1=CC=C(C=NNC2=C3C=CSC3=CC=N2)C=C1F NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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, 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: [3, 1, 3, 1, 1, 1, 1, 1, 10, 10, 48, 116, 116, 117, 116, 116, 116, 116, 116, 1, 1, 1, 1, 1, 10, 48, 116, 117, 116, 116, 1] 117
rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29])
total number of confs: 219
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040042 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040042
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040042/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040042
Building REAL300000040043
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040043'
/scratch/stefan/7769621/working/building/REAL300000040043 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040043

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040043/0 /scratch/stefan/7769621/working/building/REAL300000040043 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 59)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/59
`/scratch/stefan/7769621/working/3D/59' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C=CC1=CC=C(C=NNC2=C3C=CSC3=CC=N2)O1)

`REAL300000040043.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040043.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040043/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040043 none O=C([O-])C=CC1=CC=C(C=NNC2=C3C=CSC3=CC=N2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [148, 148, 148, 148, 86, 86, 86, 86, 51, 51, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 86, 148, 148, 86, 86, 51, 11, 1, 1, 1, 1] 148
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 335
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040043 none O=C([O-])C=CC1=CC=C(C=NNC2=C3C=CSC3=CC=N2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [30, 12, 30, 12, 1, 1, 1, 1, 1, 1, 8, 8, 32, 86, 86, 86, 86, 86, 85, 86, 86, 1, 12, 12, 1, 1, 8, 32, 86, 86, 85, 86] 148
rigid atoms, others: [4, 5, 6, 7, 8, 9, 21, 24, 25] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 232
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040043 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040043/1 /scratch/stefan/7769621/working/building/REAL300000040043 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 60)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/60
`/scratch/stefan/7769621/working/3D/60' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C=CC1=CC=C(CN=NC2=C3C=CSC3=CC=N2)O1)

`REAL300000040043.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040043.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040043/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040043 none O=C([O-])C=CC1=CC=C(CN=NC2=C3C=CSC3=CC=N2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 12, 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, 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: [200, 201, 201, 201, 104, 104, 104, 104, 29, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 104, 201, 201, 104, 104, 29, 29, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 488
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040043 none O=C([O-])C=CC1=CC=C(CN=NC2=C3C=CSC3=CC=N2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 12, 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, 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: [16, 9, 17, 9, 1, 1, 1, 1, 1, 1, 8, 71, 71, 104, 104, 104, 104, 104, 104, 104, 104, 1, 9, 9, 1, 1, 8, 8, 104, 104, 104, 104] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 21, 24, 25] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 206
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040043 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040043
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040043/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040043/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040043
Building REAL300000040044
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040044'
/scratch/stefan/7769621/working/building/REAL300000040044 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040044

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040044/0 /scratch/stefan/7769621/working/building/REAL300000040044 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 61)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/61
`/scratch/stefan/7769621/working/3D/61' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2C=CSC2=CC=N1)C1=CC(C(=O)[O-])=CC=C1OC(C)C)

`REAL300000040044.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040044.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040044/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040044 none CC(=NNC1=C2C=CSC2=CC=N1)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 50, 155, 155, 155, 155, 155, 155, 155, 155, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 20, 20, 11, 11, 11, 50, 155, 155, 155, 155, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20] 201
rigid atoms, others: [1, 34, 35, 36, 13, 14, 15, 16, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 325
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040044 none CC(=NNC1=C2C=CSC2=CC=N1)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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]
0  hydrogens 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, 40, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 155, 155, 155, 155, 155, 155, 155, 155, 155, 201, 201, 201, 40, 40, 40, 9, 1, 1, 1, 1, 155, 155, 155, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [32, 33, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 295
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040044 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040044/1 /scratch/stefan/7769621/working/building/REAL300000040044 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 62)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/62
`/scratch/stefan/7769621/working/3D/62' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)OC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=C2C=CSC2=CC=N1)

`REAL300000040044.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040044.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040044/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040044 none CC(C)OC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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, 2, 2, 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, 199, 201, 135, 135, 135, 135, 135, 135, 135, 135, 135, 54, 7, 54, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 135, 135, 135, 54, 54, 54, 54, 1, 1, 1, 1] 201
rigid atoms, others: [40, 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])
total number of confs: 418
number of broken/clashed sets: 28
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040044 none CC(C)OC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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, 2, 2, 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: [18, 8, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 53, 53, 135, 135, 135, 135, 135, 135, 135, 135, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 8, 8, 8, 8, 135, 135, 135, 135] 201
rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 35] set([0, 1, 2, 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])
total number of confs: 248
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040044 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040044
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040044/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040044/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040044
Building REAL300000040045
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040045'
/scratch/stefan/7769621/working/building/REAL300000040045 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040045

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040045/0 /scratch/stefan/7769621/working/building/REAL300000040045 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 63)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/63
`/scratch/stefan/7769621/working/3D/63' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC2=C1C(=NNC1=C3C=CSC3=CC=N1)CC2)

`REAL300000040045.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040045.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040045/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040045 none O=C([O-])C1=CC=CC2=C1C(=NNC1=C3C=CSC3=CC=N1)CC2 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.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', '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, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 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, 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, 11, 11, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 4, 1, 1, 1, 1, 11, 11, 11, 11] 11
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 33, 32, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 19
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040045 none O=C([O-])C1=CC=CC2=C1C(=NNC1=C3C=CSC3=CC=N1)CC2 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.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', '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, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 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, 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, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 1, 1, 1, 1] 11
rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 33, 31] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30])
total number of confs: 27
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040045 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040045
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040045/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040045
Building REAL300000040046
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040046'
/scratch/stefan/7769621/working/building/REAL300000040046 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040046

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040046/0 /scratch/stefan/7769621/working/building/REAL300000040046 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 64)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/64
`/scratch/stefan/7769621/working/3D/64' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=C4C=CSC4=CC=N3)C=C2)C=C1)

`REAL300000040046.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040046.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040046/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040046 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=C4C=CSC4=CC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 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]
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, 90, 115, 90, 115, 115, 86, 57, 86, 86, 45, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 86, 86, 115, 115, 115, 115, 86, 86, 45, 45, 1, 1, 1, 1, 86, 86, 115, 115] 115
rigid atoms, others: [33, 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, 37, 38, 39, 40])
total number of confs: 572
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: REAL300000040046 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=C4C=CSC4=CC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 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]
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: [3, 1, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 8, 58, 59, 94, 94, 94, 94, 94, 94, 94, 94, 1, 1, 3, 3, 3, 3, 1, 1, 8, 8, 94, 94, 94, 94, 1, 1, 3, 3] 115
rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 23, 24, 38, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 39, 40])
total number of confs: 159
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040046 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=C4C=CSC4=CC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 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]
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: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 1, 2, 17, 88, 88, 115, 115, 115, 115, 115, 115, 115, 115, 3, 3, 1, 1, 1, 1, 3, 3, 17, 17, 115, 115, 115, 115, 3, 3, 1, 1] 115
rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 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: 201
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040046 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040046/1 /scratch/stefan/7769621/working/building/REAL300000040046 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 65)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/65
`/scratch/stefan/7769621/working/3D/65' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=C4C=CSC4=CC=N3)C=C2)C=C1)

`REAL300000040046.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040046.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040046/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040046 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=C4C=CSC4=CC=N3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [75, 71, 75, 71, 75, 75, 64, 60, 64, 64, 58, 58, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 64, 64, 75, 75, 75, 75, 64, 64, 58, 13, 1, 1, 1, 1, 64, 64, 75, 75] 75
rigid atoms, others: [33, 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, 37, 38, 39, 40])
total number of confs: 156
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: REAL300000040046 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=C4C=CSC4=CC=N3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 35, 63, 63, 63, 63, 63, 63, 63, 63, 1, 1, 3, 3, 3, 3, 1, 1, 7, 35, 63, 63, 63, 63, 1, 1, 3, 3] 75
rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 23, 24, 38, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 39, 40])
total number of confs: 126
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040046 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=C4C=CSC4=CC=N3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 1, 3, 15, 15, 52, 75, 75, 75, 75, 75, 75, 75, 75, 3, 3, 1, 1, 1, 1, 3, 3, 15, 52, 75, 75, 75, 75, 3, 3, 1, 1] 75
rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 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: 172
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040046 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040046
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040046/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040046/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040046
Building REAL300000040047
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040047'
/scratch/stefan/7769621/working/building/REAL300000040047 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040047

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040047/0 /scratch/stefan/7769621/working/building/REAL300000040047 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 66)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/66
`/scratch/stefan/7769621/working/3D/66' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2C=CSC2=CC=N1)C1=CN=CC(C(=O)[O-])=C1)

`REAL300000040047.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040047.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040047/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040047 none CC(=NNC1=C2C=CSC2=CC=N1)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 14, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 11, 11, 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, 7, 7, 7, 3, 7, 7, 3, 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: [12, 1, 12, 12, 60, 91, 91, 91, 91, 91, 91, 91, 91, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 12, 12, 60, 91, 91, 91, 91, 1, 1, 1] 91
rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 203
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040047 none CC(=NNC1=C2C=CSC2=CC=N1)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 14, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 11, 11, 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, 7, 7, 7, 3, 7, 7, 3, 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: [47, 47, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 91, 91, 91, 91, 91, 91, 91, 91, 48, 48, 48, 12, 1, 1, 1, 1, 91, 91, 91] 91
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([0, 1, 2, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31])
total number of confs: 146
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040047 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040047
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040047/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040047
Building REAL300000040048
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040048'
/scratch/stefan/7769621/working/building/REAL300000040048 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040048

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040048/0 /scratch/stefan/7769621/working/building/REAL300000040048 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 67)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/67
`/scratch/stefan/7769621/working/3D/67' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2NC=C(CN=NC3=C4C=CSC4=CC=N3)C2=C1)

`REAL300000040048.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040048.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040048/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040048 none O=C([O-])C1=CC=C2NC=C(CN=NC3=C4C=CSC4=CC=N3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
104  conformations in input
total number of sets (complete confs): 104
using faster count positions algorithm for large data
unique positions, atoms: [104, 104, 104, 104, 104, 104, 104, 104, 104, 50, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 104, 104, 104, 104, 104, 104, 50, 50, 1, 1, 1, 1, 104] 104
rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 240
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040048 none O=C([O-])C1=CC=C2NC=C(CN=NC3=C4C=CSC4=CC=N3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
104  conformations in input
total number of sets (complete confs): 104
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 58, 58, 104, 104, 104, 104, 104, 104, 104, 104, 1, 1, 1, 1, 1, 1, 8, 8, 104, 104, 104, 104, 1] 104
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 22, 23, 24, 25, 26, 27] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31])
total number of confs: 165
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040048 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040048/1 /scratch/stefan/7769621/working/building/REAL300000040048 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 68)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/68
`/scratch/stefan/7769621/working/3D/68' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2NC=C(C=NNC3=C4C=CSC4=CC=N3)C2=C1)

`REAL300000040048.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040048.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040048/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040048 none O=C([O-])C1=CC=C2NC=C(C=NNC3=C4C=CSC4=CC=N3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [51, 51, 51, 51, 51, 51, 51, 51, 51, 35, 35, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 51, 35, 10, 1, 1, 1, 1, 51] 51
rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 80
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040048 none O=C([O-])C1=CC=C2NC=C(C=NNC3=C4C=CSC4=CC=N3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 36, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 1, 1, 10, 36, 51, 51, 51, 51, 1] 51
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 22, 23, 24, 25, 26, 27] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31])
total number of confs: 114
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040048 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040048
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040048/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040048/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040048
Building REAL300000040049
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040049'
/scratch/stefan/7769621/working/building/REAL300000040049 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040049

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040049/0 /scratch/stefan/7769621/working/building/REAL300000040049 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 69)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/69
`/scratch/stefan/7769621/working/3D/69' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC2=C3C=CSC3=CC=N2)C=C1O)

`REAL300000040049.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040049.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040049/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040049 none O=C([O-])C1=CC=C(C=NNC2=C3C=CSC3=CC=N2)C=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [91, 91, 91, 91, 91, 91, 52, 52, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 91, 91, 91, 91, 91, 52, 12, 1, 1, 1, 1, 91, 182] 182
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 30, 31])
total number of confs: 332
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040049 none O=C([O-])C1=CC=C(C=NNC2=C3C=CSC3=CC=N2)C=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [3, 1, 3, 1, 1, 1, 1, 1, 9, 9, 48, 91, 91, 91, 91, 91, 90, 91, 91, 1, 1, 1, 1, 1, 9, 48, 91, 91, 90, 91, 1, 2] 182
rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 31])
total number of confs: 187
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040049 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040049/1 /scratch/stefan/7769621/working/building/REAL300000040049 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 70)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/70
`/scratch/stefan/7769621/working/3D/70' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(CN=NC2=C3C=CSC3=CC=N2)C=C1O)

`REAL300000040049.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040049.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040049/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040049 none O=C([O-])C1=CC=C(CN=NC2=C3C=CSC3=CC=N2)C=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 12, 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, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 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, 200, 201, 199, 201, 201, 50, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 50, 50, 1, 1, 1, 1, 201, 402] 402
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 30, 31])
total number of confs: 764
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040049 none O=C([O-])C1=CC=C(CN=NC2=C3C=CSC3=CC=N2)C=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 12, 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, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 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, 1, 9, 73, 73, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 9, 9, 201, 201, 201, 201, 1, 2] 402
rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 31])
total number of confs: 300
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040049 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040049
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040049/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040049/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040049
Building REAL300000040050
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040050'
/scratch/stefan/7769621/working/building/REAL300000040050 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040050

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040050/0 /scratch/stefan/7769621/working/building/REAL300000040050 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 71)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/71
`/scratch/stefan/7769621/working/3D/71' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C=NNC2=C3C=CSC3=CC=N2)C=C1C(=O)[O-])

`REAL300000040050.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040050.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040050/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040050 none CC1=CC=C(C=NNC2=C3C=CSC3=CC=N2)C=C1C(=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.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.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, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 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
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [85, 85, 85, 84, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85, 85, 85, 85, 85, 85, 84, 50, 12, 1, 1, 1, 1, 84] 85
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 33, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 128
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040050 none CC1=CC=C(C=NNC2=C3C=CSC3=CC=N2)C=C1C(=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.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.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, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 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
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 40, 84, 84, 85, 85, 85, 84, 84, 84, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 10, 40, 84, 85, 85, 84, 1] 85
rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 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, 32])
total number of confs: 176
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040050 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040050
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040050/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040050
Building REAL300000040051
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040051'
/scratch/stefan/7769621/working/building/REAL300000040051 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040051

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040051/0 /scratch/stefan/7769621/working/building/REAL300000040051 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 72)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/72
`/scratch/stefan/7769621/working/3D/72' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Cl)SC(C=NNC2=C3C=CSC3=CC=N2)=C1)

`REAL300000040051.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040051.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040051/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040051 none O=C([O-])C1=C(Cl)SC(C=NNC2=C3C=CSC3=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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]
0  hydrogens need rotated
122  conformations in input
total number of sets (complete confs): 122
using faster count positions algorithm for large data
unique positions, atoms: [122, 122, 122, 122, 122, 122, 122, 59, 59, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 122, 59, 12, 1, 1, 1, 1, 122] 122
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 27])
total number of confs: 181
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040051 none O=C([O-])C1=C(Cl)SC(C=NNC2=C3C=CSC3=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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]
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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 11, 60, 122, 122, 122, 122, 122, 122, 122, 122, 1, 11, 60, 122, 122, 122, 122, 1] 122
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 27] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26])
total number of confs: 243
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040051 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040051
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040051/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040051
Building REAL300000040052
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040052'
/scratch/stefan/7769621/working/building/REAL300000040052 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040052

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040052/0 /scratch/stefan/7769621/working/building/REAL300000040052 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 73)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/73
`/scratch/stefan/7769621/working/3D/73' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2C=CSC2=CC=N1)C1=CC=C(C(=O)[O-])C=C1C)

`REAL300000040052.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040052.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040052/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040052 none CC(=NNC1=C2C=CSC2=CC=N1)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 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, 2, 2, 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: [9, 1, 9, 9, 40, 60, 60, 60, 60, 60, 60, 60, 60, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 9, 40, 60, 60, 60, 60, 1, 1, 1, 2, 2, 2] 60
rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 17, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36])
total number of confs: 141
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040052 none CC(=NNC1=C2C=CSC2=CC=N1)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 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, 2, 2, 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: [41, 42, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 60, 60, 42, 42, 60, 60, 60, 60, 60, 42, 42, 42, 13, 1, 1, 1, 1, 60, 60, 60, 60, 60, 60] 60
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36])
total number of confs: 215
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040052 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040052/1 /scratch/stefan/7769621/working/building/REAL300000040052 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 74)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/74
`/scratch/stefan/7769621/working/3D/74' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(=O)[O-])=CC=C1C(C)N=NC1=C2C=CSC2=CC=N1)

`REAL300000040052.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040052.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040052/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040052 none CC1=CC(C(=O)[O-])=CC=C1C(C)N=NC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 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
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [43, 43, 43, 35, 43, 43, 43, 43, 43, 35, 7, 35, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 35, 35, 35, 35, 1, 1, 1, 1] 43
rigid atoms, others: [33, 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])
total number of confs: 163
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040052 none CC1=CC(C(=O)[O-])=CC=C1C(C)N=NC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 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
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 30, 30, 43, 43, 43, 43, 43, 43, 43, 43, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 43, 43, 43, 43] 43
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 75
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040052 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040052
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040052/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040052/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040052
Building REAL300000040053
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040053'
/scratch/stefan/7769621/working/building/REAL300000040053 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040053

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040053/0 /scratch/stefan/7769621/working/building/REAL300000040053 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 75)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/75
`/scratch/stefan/7769621/working/3D/75' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C(Cl)C=C1C=NNC1=C2C=CSC2=CC=N1)

`REAL300000040053.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040053.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040053/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040053 none O=C([O-])C1=CN=C(Cl)C=C1C=NNC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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, 8, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [54, 54, 54, 54, 54, 38, 54, 54, 54, 38, 38, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 38, 11, 1, 1, 1, 1] 54
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25])
total number of confs: 131
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040053 none O=C([O-])C1=CN=C(Cl)C=C1C=NNC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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, 8, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 28, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1, 6, 28, 54, 54, 54, 54] 54
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29])
total number of confs: 114
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040053 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040053
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040053/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040053
Building REAL300000040054
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040054'
/scratch/stefan/7769621/working/building/REAL300000040054 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040054

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040054/0 /scratch/stefan/7769621/working/building/REAL300000040054 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 76)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/76
`/scratch/stefan/7769621/working/3D/76' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=C(C(=O)[O-])C=C1C=NNC1=C2C=CSC2=CC=N1)

`REAL300000040054.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040054.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040054/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040054 none CN1N=C(C(=O)[O-])C=C1C=NNC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [51, 51, 51, 51, 51, 51, 51, 51, 38, 38, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 38, 12, 1, 1, 1, 1] 51
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26])
total number of confs: 86
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040054 none CN1N=C(C(=O)[O-])C=C1C=NNC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 27, 51, 51, 51, 51, 51, 50, 51, 51, 2, 2, 2, 1, 8, 27, 51, 51, 50, 51] 51
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30])
total number of confs: 118
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040054 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040054
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040054/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040054
Building REAL300000040055
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040055'
/scratch/stefan/7769621/working/building/REAL300000040055 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040055

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040055/0 /scratch/stefan/7769621/working/building/REAL300000040055 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 77)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/77
`/scratch/stefan/7769621/working/3D/77' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C2=CC=C(C=NNC3=C4C=CSC4=CC=N3)O2)=CC=C1O)

`REAL300000040055.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040055.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040055/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040055 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=C4C=CSC4=CC=N3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 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, 82, 82, 82, 82, 48, 48, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 82, 201, 201, 201, 201, 201, 82, 82, 48, 11, 1, 1, 1, 1, 201, 201, 402] 402
rigid atoms, others: [32, 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, 36, 37, 38])
total number of confs: 683
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: REAL300000040055 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=C4C=CSC4=CC=N3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 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: [25, 13, 25, 13, 13, 1, 1, 1, 1, 1, 1, 6, 6, 29, 82, 82, 82, 82, 82, 81, 82, 82, 1, 13, 13, 12, 12, 13, 1, 1, 6, 29, 82, 82, 81, 82, 13, 13, 26] 402
rigid atoms, others: [5, 6, 7, 8, 9, 10, 22, 28, 29] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 231
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040055 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=C4C=CSC4=CC=N3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 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, 50, 50, 133, 201, 201, 201, 201, 201, 201, 201, 201, 13, 1, 1, 1, 1, 1, 13, 13, 50, 133, 201, 201, 201, 201, 1, 1, 2] 402
rigid atoms, others: [1, 3, 4, 5, 6, 23, 24, 25, 26, 27, 37, 36] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 38])
total number of confs: 463
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040055 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040055/1 /scratch/stefan/7769621/working/building/REAL300000040055 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 78)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/78
`/scratch/stefan/7769621/working/3D/78' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C2=CC=C(CN=NC3=C4C=CSC4=CC=N3)O2)=CC=C1O)

`REAL300000040055.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040055.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040055/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040055 none O=C([O-])C1=CC(C2=CC=C(CN=NC3=C4C=CSC4=CC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 12, 1, 1, 1, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 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, 108, 108, 108, 108, 28, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 108, 201, 201, 201, 201, 201, 108, 108, 28, 28, 1, 1, 1, 1, 201, 201, 402] 402
rigid atoms, others: [32, 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, 36, 37, 38])
total number of confs: 724
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: REAL300000040055 none O=C([O-])C1=CC(C2=CC=C(CN=NC3=C4C=CSC4=CC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 12, 1, 1, 1, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 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: [13, 12, 13, 12, 12, 1, 1, 1, 1, 1, 1, 8, 75, 75, 108, 108, 108, 108, 108, 108, 108, 108, 1, 12, 12, 11, 11, 12, 1, 1, 8, 8, 108, 108, 108, 108, 12, 12, 24] 402
rigid atoms, others: [5, 6, 7, 8, 9, 10, 22, 28, 29] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 208
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040055 none O=C([O-])C1=CC(C2=CC=C(CN=NC3=C4C=CSC4=CC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 12, 1, 1, 1, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 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, 12, 12, 12, 12, 57, 200, 200, 201, 201, 201, 201, 201, 201, 201, 201, 12, 1, 1, 1, 1, 1, 12, 12, 57, 57, 201, 201, 201, 201, 1, 1, 2] 402
rigid atoms, others: [1, 3, 4, 5, 6, 23, 24, 25, 26, 27, 37, 36] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 38])
total number of confs: 377
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040055 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040055
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040055/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040055/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040055
Building REAL300000040056
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040056'
/scratch/stefan/7769621/working/building/REAL300000040056 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040056

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040056/0 /scratch/stefan/7769621/working/building/REAL300000040056 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 79)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/79
`/scratch/stefan/7769621/working/3D/79' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C(=O)[O-])C=C1C=NNC1=C2C=CSC2=CC=N1)

`REAL300000040056.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040056.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040056/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040056 none CN1C=C(C(=O)[O-])C=C1C=NNC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 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
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, 55, 55, 42, 42, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 42, 12, 1, 1, 1, 1] 55
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 92
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040056 none CN1C=C(C(=O)[O-])C=C1C=NNC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 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
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 30, 55, 55, 55, 55, 55, 54, 55, 55, 2, 2, 2, 1, 1, 8, 30, 55, 55, 54, 55] 55
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 123
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040056 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040056/1 /scratch/stefan/7769621/working/building/REAL300000040056 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 80)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/80
`/scratch/stefan/7769621/working/3D/80' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C(=O)[O-])C=C1CN=NC1=C2C=CSC2=CC=N1)

`REAL300000040056.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040056.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040056/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040056 none CN1C=C(C(=O)[O-])C=C1CN=NC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 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
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, 119, 119, 119, 119, 48, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 119, 48, 48, 1, 1, 1, 1] 119
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 255
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040056 none CN1C=C(C(=O)[O-])C=C1CN=NC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 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
119  conformations in input
total number of sets (complete confs): 119
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 69, 69, 119, 119, 119, 119, 119, 119, 119, 119, 2, 2, 2, 1, 1, 9, 9, 119, 119, 119, 119] 119
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 192
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040056 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040056
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040056/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040056/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040056
Building REAL300000040057
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040057'
/scratch/stefan/7769621/working/building/REAL300000040057 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040057

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040057/0 /scratch/stefan/7769621/working/building/REAL300000040057 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 81)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/81
`/scratch/stefan/7769621/working/3D/81' -> `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=NNC1=C2C=CSC2=CC=N1)

`REAL300000040057.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040057.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040057/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040057 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=C2C=CSC2=CC=N1 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.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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, 2, 2, 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, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 8, 1, 1, 1, 1] 20
rigid atoms, others: [35, 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])
total number of confs: 34
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040057 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=C2C=CSC2=CC=N1 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.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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, 2, 2, 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, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 4, 4, 12, 20, 20, 20, 20, 20, 20, 20, 20, 2, 2, 2, 2, 2, 2, 1, 1, 1, 4, 12, 20, 20, 20, 20] 20
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 10, 11, 12, 32, 30, 31] set([8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38])
total number of confs: 60
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040057 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040057
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040057/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040057
Building REAL300000040058
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040058'
/scratch/stefan/7769621/working/building/REAL300000040058 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040058

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040058/0 /scratch/stefan/7769621/working/building/REAL300000040058 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 82)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/82
`/scratch/stefan/7769621/working/3D/82' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])C=C(C=NNC2=C3C=CSC3=CC=N2)O1)

`REAL300000040058.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040058.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040058/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040058 none CC1=C(C(=O)[O-])C=C(C=NNC2=C3C=CSC3=CC=N2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [94, 94, 94, 94, 94, 94, 94, 48, 48, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 93, 94, 94, 94, 94, 48, 11, 1, 1, 1, 1] 94
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 144
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040058 none CC1=C(C(=O)[O-])C=C(C=NNC2=C3C=CSC3=CC=N2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 8, 8, 47, 94, 93, 94, 94, 94, 94, 94, 94, 1, 2, 2, 2, 1, 8, 47, 94, 93, 94, 94] 94
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 20, 24] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30])
total number of confs: 198
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040058 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040058
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040058/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040058
Building REAL300000040059
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040059'
/scratch/stefan/7769621/working/building/REAL300000040059 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040059

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040059/0 /scratch/stefan/7769621/working/building/REAL300000040059 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 83)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/83
`/scratch/stefan/7769621/working/3D/83' -> `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=NNC3=C4C=CSC4=CC=N3)S2)C=C1)

`REAL300000040059.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040059.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040059/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040059 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=C4C=CSC4=CC=N3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need 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, 144, 201, 201, 144, 144, 144, 144, 63, 63, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 144, 201, 201, 201, 201, 144, 144, 63, 13, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [32, 33, 34, 35, 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, 36, 37])
total number of confs: 677
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: REAL300000040059 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=C4C=CSC4=CC=N3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens 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, 12, 12, 57, 144, 144, 144, 144, 144, 143, 144, 144, 1, 7, 7, 7, 7, 1, 1, 12, 57, 144, 144, 143, 144, 7, 7] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 23, 28, 29] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 294
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040059 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=C4C=CSC4=CC=N3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 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, 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: [2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 7, 7, 38, 38, 88, 120, 120, 120, 120, 120, 120, 120, 120, 7, 1, 1, 1, 1, 7, 7, 38, 88, 120, 120, 120, 120, 1, 1] 120
rigid atoms, others: [1, 3, 4, 5, 6, 7, 24, 25, 26, 27, 37, 36] 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])
total number of confs: 272
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040059 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040059/1 /scratch/stefan/7769621/working/building/REAL300000040059 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 84)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/84
`/scratch/stefan/7769621/working/3D/84' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=C4C=CSC4=CC=N3)S2)C=C1)

`REAL300000040059.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040059.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040059/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040059 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=C4C=CSC4=CC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 14, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 149, 201, 149, 201, 201, 111, 111, 111, 111, 36, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 111, 201, 201, 201, 201, 111, 111, 36, 36, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [32, 33, 34, 35, 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, 36, 37])
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: REAL300000040059 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=C4C=CSC4=CC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 14, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 8, 69, 69, 111, 111, 111, 111, 111, 111, 111, 111, 1, 7, 7, 7, 7, 1, 1, 8, 8, 111, 111, 111, 111, 7, 7] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 23, 28, 29] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 198
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040059 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=C4C=CSC4=CC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 14, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 7, 7, 44, 167, 167, 201, 201, 201, 201, 201, 201, 201, 201, 7, 1, 1, 1, 1, 7, 7, 44, 44, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 24, 25, 26, 27, 37, 36] 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])
total number of confs: 358
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040059 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040059
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040059/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040059/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040059
Building REAL300000040060
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040060'
/scratch/stefan/7769621/working/building/REAL300000040060 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040060

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040060/0 /scratch/stefan/7769621/working/building/REAL300000040060 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 85)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/85
`/scratch/stefan/7769621/working/3D/85' -> `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=NNC3=C4C=CSC4=CC=N3)S2)=C1)

`REAL300000040060.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040060.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040060/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040060 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=C4C=CSC4=CC=N3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.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, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
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, 108, 108, 108, 108, 51, 51, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 108, 201, 201, 201, 201, 108, 108, 51, 11, 1, 1, 1, 1, 201] 201
rigid atoms, others: [33, 34, 35, 36, 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, 37])
total number of confs: 303
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: REAL300000040060 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=C4C=CSC4=CC=N3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.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, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens 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, 12, 13, 13, 1, 1, 1, 1, 1, 1, 10, 10, 41, 108, 108, 108, 108, 108, 107, 108, 108, 1, 13, 12, 13, 13, 1, 1, 10, 41, 108, 108, 107, 108, 13] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 24, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 211
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040060 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=C4C=CSC4=CC=N3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.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, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 13, 12, 12, 13, 66, 66, 145, 201, 201, 201, 201, 201, 201, 201, 201, 13, 1, 1, 1, 1, 13, 13, 66, 146, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28, 37] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 470
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040060 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040060/1 /scratch/stefan/7769621/working/building/REAL300000040060 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 86)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/86
`/scratch/stefan/7769621/working/3D/86' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(C2=CC=C(CN=NC3=C4C=CSC4=CC=N3)S2)=C1)

`REAL300000040060.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040060.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040060/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040060 none O=C([O-])C1=CC=CC(C2=CC=C(CN=NC3=C4C=CSC4=CC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.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, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 14, 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, 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, 201, 76, 76, 76, 76, 18, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 76, 201, 201, 201, 201, 76, 76, 18, 18, 1, 1, 1, 1, 201] 201
rigid atoms, others: [33, 34, 35, 36, 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, 37])
total number of confs: 319
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: REAL300000040060 none O=C([O-])C1=CC=CC(C2=CC=C(CN=NC3=C4C=CSC4=CC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.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, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 14, 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, 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: [12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 8, 64, 64, 76, 76, 76, 76, 76, 76, 76, 76, 1, 12, 12, 12, 12, 1, 1, 8, 8, 76, 76, 76, 76, 12] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 24, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 124
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040060 none O=C([O-])C1=CC=CC(C2=CC=C(CN=NC3=C4C=CSC4=CC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.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, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 54, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 12, 1, 1, 1, 1, 12, 12, 54, 54, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28, 37] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 355
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040060 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040060
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040060/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040060/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040060
Building REAL300000040061
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040061'
/scratch/stefan/7769621/working/building/REAL300000040061 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040061

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040061/0 /scratch/stefan/7769621/working/building/REAL300000040061 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 87)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/87
`/scratch/stefan/7769621/working/3D/87' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC(C(=O)[O-])=C(C=NNC2=C3C=CSC3=CC=N2)S1)

`REAL300000040061.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040061.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040061/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040061 none CCC1=CC(C(=O)[O-])=C(C=NNC2=C3C=CSC3=CC=N2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 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, 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: [112, 83, 83, 83, 83, 83, 90, 90, 49, 49, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 83, 112, 112, 112, 112, 112, 83, 49, 13, 1, 1, 1, 1] 112
rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 320
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040061 none CCC1=CC(C(=O)[O-])=C(C=NNC2=C3C=CSC3=CC=N2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 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, 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: [8, 1, 1, 1, 1, 1, 3, 3, 1, 1, 5, 5, 33, 83, 83, 83, 83, 83, 83, 83, 83, 1, 8, 8, 8, 8, 8, 1, 5, 33, 83, 83, 83, 83] 112
rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 21, 27] set([0, 6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33])
total number of confs: 171
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040061 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040061
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040061/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040061
Building REAL300000040062
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040062'
/scratch/stefan/7769621/working/building/REAL300000040062 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040062

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040062/0 /scratch/stefan/7769621/working/building/REAL300000040062 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 88)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/88
`/scratch/stefan/7769621/working/3D/88' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=NNC1=C2C=CSC2=CC=N1)

`REAL300000040062.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040062.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040062/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040062 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 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, 7]
0  hydrogens need rotated
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 47, 47, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 141, 141, 141, 141, 141, 141, 47, 9, 1, 1, 1, 1] 141
rigid atoms, others: [32, 33, 34, 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: 190
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040062 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 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, 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: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 12, 12, 65, 141, 141, 141, 141, 141, 140, 141, 141, 4, 4, 4, 1, 1, 1, 12, 65, 141, 141, 141, 141] 141
rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 26, 27, 28] set([0, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34])
total number of confs: 289
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040062 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040062
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040062/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040062
Building REAL300000040063
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040063'
/scratch/stefan/7769621/working/building/REAL300000040063 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040063

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040063/0 /scratch/stefan/7769621/working/building/REAL300000040063 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 89)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/89
`/scratch/stefan/7769621/working/3D/89' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2SC=C(C=NNC3=C4C=CSC4=CC=N3)C2=C1)

`REAL300000040063.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040063.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040063/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040063 none O=C([O-])C1=CC=C2SC=C(C=NNC3=C4C=CSC4=CC=N3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 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, 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, 57, 57, 57, 45, 45, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 45, 12, 1, 1, 1, 1, 57] 57
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 88
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040063 none O=C([O-])C1=CC=C2SC=C(C=NNC3=C4C=CSC4=CC=N3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 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, 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, 1, 1, 1, 8, 8, 28, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 8, 28, 57, 57, 57, 57, 1] 57
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 33, 22, 23, 24, 25, 26] set([0, 32, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31])
total number of confs: 119
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040063 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040063
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040063/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040063
Building REAL300000040064
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040064'
/scratch/stefan/7769621/working/building/REAL300000040064 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040064

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040064/0 /scratch/stefan/7769621/working/building/REAL300000040064 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 90)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/90
`/scratch/stefan/7769621/working/3D/90' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2CCCC(=NNC3=C4C=CSC4=CC=N3)C2=C1)

`REAL300000040064.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040064.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040064/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040064 none O=C([O-])C1=CN=C2CCCC(=NNC3=C4C=CSC4=CC=N3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 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, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 15] 15
rigid atoms, others: [32, 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, 36])
total number of confs: 24
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040064 none O=C([O-])C1=CN=C2CCCC(=NNC3=C4C=CSC4=CC=N3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 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, 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, 1, 1, 1, 1, 1, 9, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 15, 15, 15, 15, 1] 15
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36] set([0, 32, 2, 34, 35, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31])
total number of confs: 33
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040064 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040064
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040064/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040064
Building REAL300000040065
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040065'
/scratch/stefan/7769621/working/building/REAL300000040065 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040065

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040065/0 /scratch/stefan/7769621/working/building/REAL300000040065 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 91)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/91
`/scratch/stefan/7769621/working/3D/91' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(Br)C(C=NNC2=C3C=CSC3=CC=N2)=C1)

`REAL300000040065.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040065.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040065/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040065 none O=C([O-])C1=CC=C(Br)C(C=NNC2=C3C=CSC3=CC=N2)=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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 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]
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, 70, 70, 43, 43, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 43, 10, 1, 1, 1, 1, 70] 70
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 30])
total number of confs: 107
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040065 none O=C([O-])C1=CC=C(Br)C(C=NNC2=C3C=CSC3=CC=N2)=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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 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]
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, 1, 1, 11, 11, 51, 70, 70, 70, 70, 70, 70, 70, 70, 1, 1, 1, 11, 51, 70, 70, 70, 70, 1] 70
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 30] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29])
total number of confs: 160
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040065 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040065
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040065/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040065
Building REAL300000040066
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040066'
/scratch/stefan/7769621/working/building/REAL300000040066 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040066

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040066/0 /scratch/stefan/7769621/working/building/REAL300000040066 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 92)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/92
`/scratch/stefan/7769621/working/3D/92' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C=NNC2=C3C=CSC3=CC=N2)C(C(=O)[O-])=C1)

`REAL300000040066.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040066.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040066/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040066 none CC1=CC=C(C=NNC2=C3C=CSC3=CC=N2)C(C(=O)[O-])=C1 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.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [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]
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, 44, 44, 44, 30, 30, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 30, 10, 1, 1, 1, 1, 44] 44
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 33, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 73
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040066 none CC1=CC=C(C=NNC2=C3C=CSC3=CC=N2)C(C(=O)[O-])=C1 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.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 26, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 3, 3, 1, 2, 2, 2, 1, 1, 6, 26, 44, 44, 44, 44, 1] 44
rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 17, 18, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32])
total number of confs: 104
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040066 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040066
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040066/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040066
Building REAL300000040067
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040067'
/scratch/stefan/7769621/working/building/REAL300000040067 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040067

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040067/0 /scratch/stefan/7769621/working/building/REAL300000040067 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 93)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/93
`/scratch/stefan/7769621/working/3D/93' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=C3C=CSC3=CC=N2)=CC=C1C(=O)[O-])

`REAL300000040067.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040067.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040067/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040067 none COC1=CC(C=NNC2=C3C=CSC3=CC=N2)=CC=C1C(=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.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.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, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 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, 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: [201, 169, 169, 169, 55, 55, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 169, 169, 169, 169, 201, 201, 201, 201, 201, 169, 55, 11, 1, 1, 1, 1, 169, 169] 201
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 33, 34, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 422
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040067 none COC1=CC(C=NNC2=C3C=CSC3=CC=N2)=CC=C1C(=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.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.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, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 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, 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: [3, 1, 1, 1, 1, 1, 10, 10, 55, 169, 169, 169, 169, 169, 168, 169, 169, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 10, 55, 169, 169, 168, 169, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 33, 34, 17, 18, 19, 20, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32])
total number of confs: 294
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040067 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040067
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040067/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040067
Building REAL300000040068
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040068'
/scratch/stefan/7769621/working/building/REAL300000040068 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040068

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040068/0 /scratch/stefan/7769621/working/building/REAL300000040068 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 94)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/94
`/scratch/stefan/7769621/working/3D/94' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(F)=C(C=NNC2=C3C=CSC3=CC=N2)C(F)=C1)

`REAL300000040068.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040068.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040068/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040068 none O=C([O-])C1=CC(F)=C(C=NNC2=C3C=CSC3=CC=N2)C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 40, 40, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 40, 13, 1, 1, 1, 1, 42] 42
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 30])
total number of confs: 68
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040068 none O=C([O-])C1=CC(F)=C(C=NNC2=C3C=CSC3=CC=N2)C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 26, 42, 42, 42, 42, 42, 41, 42, 42, 1, 1, 1, 1, 7, 26, 42, 42, 41, 42, 1] 42
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 30] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29])
total number of confs: 100
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040068 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040068
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040068/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040068
Building REAL300000040069
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040069'
/scratch/stefan/7769621/working/building/REAL300000040069 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040069

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040069/0 /scratch/stefan/7769621/working/building/REAL300000040069 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 95)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/95
`/scratch/stefan/7769621/working/3D/95' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])NC(C=NNC2=C3C=CSC3=CC=N2)=C1)

`REAL300000040069.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040069.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040069/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040069 none CC1=C(C(=O)[O-])NC(C=NNC2=C3C=CSC3=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 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]
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, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 89, 89, 50, 12, 1, 1, 1, 1, 89] 89
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 135
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040069 none CC1=C(C(=O)[O-])NC(C=NNC2=C3C=CSC3=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 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]
0  hydrogens need rotated
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 8, 8, 44, 89, 89, 89, 89, 89, 89, 89, 89, 1, 2, 2, 2, 1, 8, 43, 89, 89, 89, 89, 1] 89
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 20, 24, 31] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30])
total number of confs: 187
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040069 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040069/1 /scratch/stefan/7769621/working/building/REAL300000040069 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 96)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/96
`/scratch/stefan/7769621/working/3D/96' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])NC(CN=NC2=C3C=CSC3=CC=N2)=C1)

`REAL300000040069.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040069.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040069/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040069 none CC1=C(C(=O)[O-])NC(CN=NC2=C3C=CSC3=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [199, 201, 201, 201, 201, 201, 201, 51, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 51, 51, 1, 1, 1, 1, 201] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 370
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040069 none CC1=C(C(=O)[O-])NC(CN=NC2=C3C=CSC3=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 9, 83, 83, 201, 201, 201, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 9, 9, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 20, 24, 31] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30])
total number of confs: 304
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040069 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040069
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040069/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040069/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040069
Building REAL300000040070
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040070'
/scratch/stefan/7769621/working/building/REAL300000040070 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040070

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040070/0 /scratch/stefan/7769621/working/building/REAL300000040070 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 97)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/97
`/scratch/stefan/7769621/working/3D/97' -> `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=NNC2=C3C=CSC3=CC=N2)=C1)

`REAL300000040070.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040070.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040070/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040070 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=C3C=CSC3=CC=N2)=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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [65, 65, 65, 65, 65, 65, 65, 65, 65, 37, 37, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 130, 37, 9, 1, 1, 1, 1, 65] 130
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 31])
total number of confs: 226
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040070 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=C3C=CSC3=CC=N2)=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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
130  conformations in input
total number of sets (complete confs): 130
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 44, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 2, 12, 44, 65, 65, 65, 65, 1] 130
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 147
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040070 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040070/1 /scratch/stefan/7769621/working/building/REAL300000040070 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 98)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/98
`/scratch/stefan/7769621/working/3D/98' -> `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=NNC2=C3C=CSC3=CC=N2)=C1)

`REAL300000040070.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040070.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040070/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040070 none O=C([O-])C1=CC(Br)=C([O-])C(C=NNC2=C3C=CSC3=CC=N2)=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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 18, 18, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 18, 8, 1, 1, 1, 1, 22] 22
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 30])
total number of confs: 37
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040070 none O=C([O-])C1=CC(Br)=C([O-])C(C=NNC2=C3C=CSC3=CC=N2)=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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 6, 18, 22, 22, 22, 22, 1] 22
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29])
total number of confs: 50
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040070 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040070
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040070/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040070/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040070
Building REAL300000040071
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040071'
/scratch/stefan/7769621/working/building/REAL300000040071 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040071

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040071/0 /scratch/stefan/7769621/working/building/REAL300000040071 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 99)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/99
`/scratch/stefan/7769621/working/3D/99' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(COC2=CC=C(CN=NC3=C4C=CSC4=CC=N3)C=C2)O1)

`REAL300000040071.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040071.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040071/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040071 none O=C([O-])C1=CC=C(COC2=CC=C(CN=NC3=C4C=CSC4=CC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 12, 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, 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]
0  hydrogens need rotated
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, 94, 94, 44, 25, 94, 94, 25, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 94, 94, 201, 201, 201, 94, 94, 94, 94, 25, 25, 1, 1, 1, 1, 94, 94] 201
rigid atoms, others: [36, 37, 38, 39, 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, 40, 41])
total number of confs: 553
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: REAL300000040071 none O=C([O-])C1=CC=C(COC2=CC=C(CN=NC3=C4C=CSC4=CC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 12, 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, 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]
0  hydrogens 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, 7, 8, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 73, 73, 94, 94, 94, 94, 94, 94, 94, 94, 1, 1, 7, 7, 7, 1, 1, 1, 1, 9, 9, 94, 94, 94, 94, 1, 1] 201
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 40, 41, 25, 26, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 34, 35, 36, 37, 38, 39])
total number of confs: 153
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040071 none O=C([O-])C1=CC=C(COC2=CC=C(CN=NC3=C4C=CSC4=CC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 12, 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, 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]
0  hydrogens 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, 7, 7, 38, 190, 190, 201, 201, 201, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 7, 7, 7, 7, 38, 38, 201, 201, 201, 201, 7, 7] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 345
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040071 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040071/1 /scratch/stefan/7769621/working/building/REAL300000040071 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 100)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/100
`/scratch/stefan/7769621/working/3D/100' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=C4C=CSC4=CC=N3)C=C2)O1)

`REAL300000040071.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040071.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040071/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040071 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=C4C=CSC4=CC=N3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 133, 118, 89, 72, 118, 117, 42, 42, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 118, 118, 201, 201, 201, 133, 133, 118, 117, 42, 8, 1, 1, 1, 1, 118, 118] 201
rigid atoms, others: [36, 37, 38, 39, 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, 40, 41])
total number of confs: 563
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040071 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=C4C=CSC4=CC=N3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 14, 14, 15, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 47, 117, 117, 118, 117, 117, 117, 117, 117, 1, 1, 14, 15, 15, 5, 5, 1, 1, 10, 47, 117, 118, 117, 118, 1, 1] 201
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 40, 41, 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, 34, 35, 36, 37, 38, 39])
total number of confs: 247
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040071 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=C4C=CSC4=CC=N3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 14, 14, 14, 14, 14, 61, 61, 150, 201, 201, 201, 201, 201, 201, 201, 201, 14, 14, 1, 1, 1, 8, 8, 15, 15, 62, 150, 201, 201, 201, 201, 14, 14] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 495
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040071 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040071
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040071/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040071/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040071
Building REAL300000040072
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040072'
/scratch/stefan/7769621/working/building/REAL300000040072 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040072

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040072/0 /scratch/stefan/7769621/working/building/REAL300000040072 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 101)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/101
`/scratch/stefan/7769621/working/3D/101' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=C3C=CSC3=CC=N2)=C1O)

`REAL300000040072.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040072.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040072/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040072 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=C3C=CSC3=CC=N2)=C1O 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.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', '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, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
150  conformations in input
total number of sets (complete confs): 150
using faster count positions algorithm for large data
unique positions, atoms: [75, 75, 75, 75, 75, 75, 75, 75, 75, 75, 75, 42, 42, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 75, 75, 42, 12, 1, 1, 1, 1, 150] 150
rigid atoms, others: [33, 34, 35, 36, 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, 37])
total number of confs: 267
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040072 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=C3C=CSC3=CC=N2)=C1O 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.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', '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, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
150  conformations in input
total number of sets (complete confs): 150
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 41, 75, 75, 75, 75, 75, 75, 75, 75, 1, 1, 1, 1, 1, 1, 1, 11, 41, 75, 75, 75, 75, 2] 150
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30] set([0, 32, 2, 34, 36, 37, 35, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31])
total number of confs: 157
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040072 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040072
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040072/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040072
Building REAL300000040073
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040073'
/scratch/stefan/7769621/working/building/REAL300000040073 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040073

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040073/0 /scratch/stefan/7769621/working/building/REAL300000040073 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 102)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/102
`/scratch/stefan/7769621/working/3D/102' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CC1=CC=CC(C2=CC=C(CN=NC3=C4C=CSC4=CC=N3)C=C2)=C1)

`REAL300000040073.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040073.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040073/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040073 none O=C([O-])CC1=CC=CC(C2=CC=C(CN=NC3=C4C=CSC4=CC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 146, 146, 144, 146, 146, 43, 29, 85, 85, 26, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 85, 85, 146, 201, 201, 146, 146, 146, 85, 85, 26, 26, 1, 1, 1, 1, 85, 85, 146] 201
rigid atoms, others: [37, 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, 41, 42, 43])
total number of confs: 750
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: REAL300000040073 none O=C([O-])CC1=CC=CC(C2=CC=C(CN=NC3=C4C=CSC4=CC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 5, 11, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 8, 62, 63, 86, 86, 86, 86, 86, 86, 86, 86, 1, 1, 3, 5, 5, 3, 3, 3, 1, 1, 8, 8, 86, 86, 86, 86, 1, 1, 3] 201
rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 41, 25, 26, 42] 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, 35, 36, 37, 38, 39, 40, 43])
total number of confs: 170
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040073 none O=C([O-])CC1=CC=CC(C2=CC=C(CN=NC3=C4C=CSC4=CC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 17, 117, 117, 146, 146, 146, 146, 146, 146, 146, 146, 3, 3, 1, 2, 2, 1, 1, 1, 3, 3, 17, 17, 146, 146, 146, 146, 3, 3, 1] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 43, 27, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 253
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040073 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040073/1 /scratch/stefan/7769621/working/building/REAL300000040073 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 103)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/103
`/scratch/stefan/7769621/working/3D/103' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=C4C=CSC4=CC=N3)C=C2)=C1)

`REAL300000040073.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040073.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040073/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040073 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=C4C=CSC4=CC=N3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 139, 139, 139, 139, 139, 81, 77, 101, 101, 48, 48, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 101, 101, 139, 201, 201, 139, 139, 139, 101, 101, 48, 11, 1, 1, 1, 1, 101, 101, 139] 201
rigid atoms, others: [37, 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, 41, 42, 43])
total number of confs: 688
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: REAL300000040073 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=C4C=CSC4=CC=N3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 5, 13, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 50, 101, 101, 101, 101, 101, 101, 101, 101, 1, 1, 3, 5, 5, 3, 3, 3, 1, 1, 10, 50, 101, 101, 101, 101, 1, 1, 3] 201
rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 41, 25, 26, 42] 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, 35, 36, 37, 38, 39, 40, 43])
total number of confs: 233
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040073 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=C4C=CSC4=CC=N3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 12, 17, 84, 139, 139, 139, 139, 139, 139, 139, 139, 3, 3, 1, 2, 2, 1, 1, 1, 3, 3, 12, 83, 139, 139, 139, 139, 3, 3, 1] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 43, 27, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 307
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040073 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040073
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040073/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040073/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040073
Building REAL300000040074
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040074'
/scratch/stefan/7769621/working/building/REAL300000040074 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040074

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040074/0 /scratch/stefan/7769621/working/building/REAL300000040074 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 104)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/104
`/scratch/stefan/7769621/working/3D/104' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NNC2=C3C=CSC3=CC=N2)SC(Cl)=C1)

`REAL300000040074.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040074.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040074/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040074 none O=C([O-])C1=C(C=NNC2=C3C=CSC3=CC=N2)SC(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 14, 1, 16, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [51, 51, 51, 51, 37, 37, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 37, 11, 1, 1, 1, 1, 51] 51
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 27])
total number of confs: 83
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040074 none O=C([O-])C1=C(C=NNC2=C3C=CSC3=CC=N2)SC(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 14, 1, 16, 1, 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, 3, 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: [3, 1, 3, 1, 1, 1, 5, 5, 29, 51, 51, 51, 51, 51, 50, 51, 51, 1, 1, 1, 1, 5, 29, 51, 51, 50, 51, 1] 51
rigid atoms, others: [1, 3, 4, 5, 17, 18, 19, 20, 27] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26])
total number of confs: 111
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040074 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040074
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040074/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040074
Building REAL300000040075
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040075'
/scratch/stefan/7769621/working/building/REAL300000040075 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040075

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040075/0 /scratch/stefan/7769621/working/building/REAL300000040075 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 105)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/105
`/scratch/stefan/7769621/working/3D/105' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NNC2=C3C=CSC3=CC=N2)SC=C1)

`REAL300000040075.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040075.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040075/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040075 none O=C([O-])C1=C(C=NNC2=C3C=CSC3=CC=N2)SC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 14, 1, 1, 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, 3, 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, 31, 31, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 31, 11, 1, 1, 1, 1, 41, 41] 41
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 26, 27])
total number of confs: 70
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040075 none O=C([O-])C1=C(C=NNC2=C3C=CSC3=CC=N2)SC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 14, 1, 1, 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, 3, 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: [3, 1, 3, 1, 1, 1, 5, 5, 27, 41, 41, 41, 41, 41, 40, 41, 41, 1, 1, 1, 5, 27, 41, 41, 40, 41, 1, 1] 41
rigid atoms, others: [1, 3, 4, 5, 17, 18, 19, 26, 27] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25])
total number of confs: 95
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040075 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040075
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040075/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040075
Building REAL300000040076
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040076'
/scratch/stefan/7769621/working/building/REAL300000040076 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040076

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040076/0 /scratch/stefan/7769621/working/building/REAL300000040076 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 106)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/106
`/scratch/stefan/7769621/working/3D/106' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C=NNC2=C3C=CSC3=CC=N2)=CS1)

`REAL300000040076.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040076.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040076/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040076 none O=C([O-])C1=CC(C=NNC2=C3C=CSC3=CC=N2)=CS1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'S.3', '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, 14, 1, 1, 1, 8, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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]
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, 56, 57, 56, 56, 41, 41, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 41, 11, 1, 1, 1, 1, 56] 57
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 27])
total number of confs: 96
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040076 none O=C([O-])C1=CC(C=NNC2=C3C=CSC3=CC=N2)=CS1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'S.3', '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, 14, 1, 1, 1, 8, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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]
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, 6, 6, 28, 56, 56, 56, 56, 56, 56, 56, 56, 1, 1, 1, 6, 28, 56, 56, 56, 56, 1] 57
rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26])
total number of confs: 119
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040076 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040076
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040076/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040076
Building REAL300000040077
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040077'
/scratch/stefan/7769621/working/building/REAL300000040077 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040077

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040077/0 /scratch/stefan/7769621/working/building/REAL300000040077 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 107)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/107
`/scratch/stefan/7769621/working/3D/107' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC(C=NNC2=C3C=CSC3=CC=N2)=CC=C1OCC(=O)[O-])

`REAL300000040077.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040077.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040077/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040077 none CCOC1=CC(C=NNC2=C3C=CSC3=CC=N2)=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.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 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]
0  hydrogens 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, 63, 28, 28, 28, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 100, 188, 193, 193, 84, 84, 84, 84, 84, 28, 11, 3, 1, 1, 1, 1, 28, 28, 188, 188] 201
rigid atoms, others: [34, 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, 38, 39, 40, 41])
total number of confs: 768
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040077 none CCOC1=CC(C=NNC2=C3C=CSC3=CC=N2)=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.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 9, 1, 1, 1, 1, 1, 7, 7, 14, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 9, 31, 50, 50, 17, 17, 17, 17, 17, 1, 7, 14, 28, 28, 28, 28, 1, 1, 31, 31] 201
rigid atoms, others: [2, 3, 4, 5, 6, 39, 18, 19, 20, 21, 38, 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, 37, 40, 41])
total number of confs: 257
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040077 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040077/1 /scratch/stefan/7769621/working/building/REAL300000040077 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 108)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/108
`/scratch/stefan/7769621/working/3D/108' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC(CN=NC2=C3C=CSC3=CC=N2)=CC=C1OCC(=O)[O-])

`REAL300000040077.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040077.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040077/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040077 none CCOC1=CC(CN=NC2=C3C=CSC3=CC=N2)=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.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 48, 48, 48, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 191, 201, 201, 201, 95, 95, 95, 95, 95, 48, 11, 11, 1, 1, 1, 1, 48, 48, 201, 201] 201
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 422
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040077 none CCOC1=CC(CN=NC2=C3C=CSC3=CC=N2)=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.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 3, 1, 1, 1, 1, 1, 6, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 7, 13, 19, 19, 3, 3, 3, 3, 3, 1, 6, 6, 48, 48, 48, 48, 1, 1, 13, 13] 201
rigid atoms, others: [2, 3, 4, 5, 6, 39, 18, 19, 20, 21, 38, 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, 37, 40, 41])
total number of confs: 131
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040077 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040077
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040077/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040077/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040077
Building REAL300000040078
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040078'
/scratch/stefan/7769621/working/building/REAL300000040078 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040078

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040078/0 /scratch/stefan/7769621/working/building/REAL300000040078 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 109)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/109
`/scratch/stefan/7769621/working/3D/109' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC1=C2C=CSC2=CC=N1)

`REAL300000040078.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040078.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040078/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040078 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC1=C2C=CSC2=CC=N1 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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 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, 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: [65, 62, 65, 62, 62, 62, 62, 158, 158, 158, 158, 158, 62, 48, 48, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 158, 158, 158, 158, 158, 158, 158, 158, 158, 62, 48, 13, 1, 1, 1, 1] 158
rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 386
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: REAL300000040078 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC1=C2C=CSC2=CC=N1 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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 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, 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: [23, 13, 23, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 33, 33, 88, 158, 158, 158, 158, 158, 158, 158, 158, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 33, 88, 158, 158, 158, 158] 158
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 372
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040078 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC1=C2C=CSC2=CC=N1 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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 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, 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, 13, 13, 13, 13, 13, 1, 1, 1, 4, 4, 18, 62, 62, 62, 62, 62, 62, 62, 62, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 4, 18, 62, 62, 62, 62] 158
rigid atoms, others: [1, 3, 4, 5, 6, 12, 13, 14, 35] set([0, 2, 7, 8, 9, 10, 11, 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])
total number of confs: 129
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040078 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040078
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040078/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040078
Building REAL300000040079
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040079'
/scratch/stefan/7769621/working/building/REAL300000040079 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040079

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040079/0 /scratch/stefan/7769621/working/building/REAL300000040079 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 110)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/110
`/scratch/stefan/7769621/working/3D/110' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C)C(C=NNC2=C3C=CSC3=CC=N2)=C1C(=O)[O-])

`REAL300000040079.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040079.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040079/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040079 none COC1=CC=C(C)C(C=NNC2=C3C=CSC3=CC=N2)=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.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 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]
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, 71, 71, 71, 71, 71, 47, 47, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 71, 71, 88, 88, 88, 88, 88, 71, 71, 71, 71, 71, 47, 13, 1, 1, 1, 1] 88
rigid atoms, others: [34, 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])
total number of confs: 213
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040079 none COC1=CC=C(C)C(C=NNC2=C3C=CSC3=CC=N2)=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.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 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]
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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 27, 71, 71, 71, 71, 71, 71, 71, 71, 1, 1, 3, 3, 4, 4, 4, 1, 1, 2, 2, 2, 7, 27, 71, 71, 71, 71] 88
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 142
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040079 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040079
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040079/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040079
Building REAL300000040080
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040080'
/scratch/stefan/7769621/working/building/REAL300000040080 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040080

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040080/0 /scratch/stefan/7769621/working/building/REAL300000040080 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 111)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/111
`/scratch/stefan/7769621/working/3D/111' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C2=CC=C(F)C=C2C(C=NNC2=C3C=CSC3=CC=N2)=C1C(=O)[O-])

`REAL300000040080.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040080.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040080/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040080 none CN1C2=CC=C(F)C=C2C(C=NNC2=C3C=CSC3=CC=N2)=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.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 11, 11, 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, 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]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [46, 46, 46, 46, 46, 46, 46, 46, 46, 40, 40, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 40, 13, 1, 1, 1, 1] 46
rigid atoms, others: [34, 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])
total number of confs: 76
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040080 none CN1C2=CC=C(F)C=C2C(C=NNC2=C3C=CSC3=CC=N2)=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.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 11, 11, 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, 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]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 3, 3, 2, 2, 2, 1, 1, 1, 6, 22, 46, 46, 46, 46] 46
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37])
total number of confs: 96
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040080 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040080
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040080/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040080
Building REAL300000040081
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040081'
/scratch/stefan/7769621/working/building/REAL300000040081 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040081

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040081/0 /scratch/stefan/7769621/working/building/REAL300000040081 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 112)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/112
`/scratch/stefan/7769621/working/3D/112' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2C=CSC2=CC=N1)C1=C(C(=O)[O-])C2=CC=CC=C2S1)

`REAL300000040081.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040081.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040081/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040081 none CC(=NNC1=C2C=CSC2=CC=N1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 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, 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
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 28, 63, 63, 63, 63, 63, 63, 63, 63, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 28, 63, 63, 63, 63, 1, 1, 1, 1] 63
rigid atoms, others: [1, 34, 35, 36, 33, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 126
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040081 none CC(=NNC1=C2C=CSC2=CC=N1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 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, 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
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [35, 36, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 36, 36, 36, 13, 1, 1, 1, 1, 63, 63, 63, 63] 63
rigid atoms, others: [32, 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, 33, 34, 35, 36])
total number of confs: 114
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040081 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040081/1 /scratch/stefan/7769621/working/building/REAL300000040081 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 113)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/113
`/scratch/stefan/7769621/working/3D/113' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=C2C=CSC2=CC=N1)C1=C(C(=O)[O-])C2=CC=CC=C2S1)

`REAL300000040081.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040081.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040081/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040081 none CC(N=NC1=C2C=CSC2=CC=N1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 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, 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
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 35, 35, 74, 74, 74, 74, 74, 74, 74, 74, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 74, 74, 74, 74, 1, 1, 1, 1] 74
rigid atoms, others: [1, 34, 35, 36, 33, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 118
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040081 none CC(N=NC1=C2C=CSC2=CC=N1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 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, 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
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [43, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 74, 74, 74, 74, 74, 74, 74, 74, 74, 74, 74, 43, 43, 43, 43, 1, 1, 1, 1, 74, 74, 74, 74] 74
rigid atoms, others: [32, 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, 33, 34, 35, 36])
total number of confs: 191
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040081 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040081
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040081/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040081/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040081
Building REAL300000040082
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040082'
/scratch/stefan/7769621/working/building/REAL300000040082 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040082

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040082/0 /scratch/stefan/7769621/working/building/REAL300000040082 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 114)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/114
`/scratch/stefan/7769621/working/3D/114' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCC1=CC=C(C=NNC2=C3C=CSC3=CC=N2)O1)

`REAL300000040082.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040082.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040082/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040082 none O=C([O-])CCC1=CC=C(C=NNC2=C3C=CSC3=CC=N2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 163, 72, 72, 72, 72, 43, 43, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 72, 201, 201, 163, 163, 72, 72, 43, 9, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 734
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040082 none O=C([O-])CCC1=CC=C(C=NNC2=C3C=CSC3=CC=N2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 19, 23, 9, 1, 1, 1, 1, 1, 1, 6, 6, 27, 72, 72, 72, 72, 72, 72, 72, 72, 1, 19, 19, 9, 9, 1, 1, 6, 27, 72, 72, 72, 72] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 21, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 232
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040082 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040082/1 /scratch/stefan/7769621/working/building/REAL300000040082 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 115)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/115
`/scratch/stefan/7769621/working/3D/115' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCC1=CC=C(CN=NC2=C3C=CSC3=CC=N2)O1)

`REAL300000040082.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040082.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040082/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040082 none O=C([O-])CCC1=CC=C(CN=NC2=C3C=CSC3=CC=N2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 12, 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, 3, 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, 201, 180, 78, 78, 78, 78, 21, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 78, 201, 201, 180, 180, 78, 78, 21, 21, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 727
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040082 none O=C([O-])CCC1=CC=C(CN=NC2=C3C=CSC3=CC=N2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 12, 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, 3, 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: [21, 13, 21, 7, 1, 1, 1, 1, 1, 1, 8, 62, 62, 78, 78, 78, 78, 78, 78, 78, 78, 1, 13, 13, 7, 7, 1, 1, 8, 8, 78, 78, 78, 78] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 21, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 205
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040082 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040082
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040082/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040082/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040082
Building REAL300000040083
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040083'
/scratch/stefan/7769621/working/building/REAL300000040083 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040083

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040083/0 /scratch/stefan/7769621/working/building/REAL300000040083 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 116)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/116
`/scratch/stefan/7769621/working/3D/116' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NNC2=C3C=CSC3=CC=N2)SC(Br)=C1)

`REAL300000040083.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040083.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040083/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040083 none O=C([O-])C1=C(C=NNC2=C3C=CSC3=CC=N2)SC(Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 14, 1, 17, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [50, 50, 50, 50, 36, 36, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 36, 11, 1, 1, 1, 1, 50] 50
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 27])
total number of confs: 82
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040083 none O=C([O-])C1=C(C=NNC2=C3C=CSC3=CC=N2)SC(Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 14, 1, 17, 1, 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, 3, 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: [3, 1, 3, 1, 1, 1, 5, 5, 29, 50, 50, 50, 50, 50, 49, 50, 50, 1, 1, 1, 1, 5, 29, 50, 50, 49, 50, 1] 50
rigid atoms, others: [1, 3, 4, 5, 17, 18, 19, 20, 27] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26])
total number of confs: 109
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040083 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040083
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040083/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040083
Building REAL300000040084
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040084'
/scratch/stefan/7769621/working/building/REAL300000040084 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040084

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040084/0 /scratch/stefan/7769621/working/building/REAL300000040084 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 117)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/117
`/scratch/stefan/7769621/working/3D/117' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C2NC=C(CN=NC3=C4C=CSC4=CC=N3)C2=CC=C1)

`REAL300000040084.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040084.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040084/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040084 none O=C([O-])C1=C2NC=C(CN=NC3=C4C=CSC4=CC=N3)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.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, 1, 1, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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, 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, 60, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 165, 165, 165, 165, 165, 165, 60, 60, 1, 1, 1, 1, 165, 165, 165] 165
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 34, 33, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 333
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040084 none O=C([O-])C1=C2NC=C(CN=NC3=C4C=CSC4=CC=N3)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.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, 1, 1, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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, 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, 3, 1, 1, 1, 1, 1, 1, 9, 78, 79, 165, 165, 165, 165, 165, 165, 165, 165, 1, 1, 1, 1, 1, 1, 9, 9, 165, 165, 165, 165, 1, 1, 1] 165
rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 33] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31])
total number of confs: 255
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040084 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040084/1 /scratch/stefan/7769621/working/building/REAL300000040084 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 118)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/118
`/scratch/stefan/7769621/working/3D/118' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C2NC=C(C=NNC3=C4C=CSC4=CC=N3)C2=CC=C1)

`REAL300000040084.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040084.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040084/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040084 none O=C([O-])C1=C2NC=C(C=NNC3=C4C=CSC4=CC=N3)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.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, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 4, 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, 7, 7, 7, 7]
0  hydrogens need rotated
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 67, 67, 67, 67, 44, 43, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 66, 43, 12, 1, 1, 1, 1, 67, 67, 67] 67
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 34, 33, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 113
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040084 none O=C([O-])C1=C2NC=C(C=NNC3=C4C=CSC4=CC=N3)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.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, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 4, 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, 7, 7, 7, 7]
0  hydrogens need rotated
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 10, 45, 66, 66, 67, 66, 66, 67, 67, 67, 1, 1, 1, 1, 1, 1, 10, 44, 67, 67, 67, 67, 1, 1, 1] 67
rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 33] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31])
total number of confs: 149
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040084 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040084
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040084/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040084/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040084
Building REAL300000040085
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040085'
/scratch/stefan/7769621/working/building/REAL300000040085 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040085

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040085/0 /scratch/stefan/7769621/working/building/REAL300000040085 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 119)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/119
`/scratch/stefan/7769621/working/3D/119' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2C=CSC2=CC=N1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1)

`REAL300000040085.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040085.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040085/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040085 none CC(=NNC1=C2C=CSC2=CC=N1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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, 14, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 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, 7, 7, 7, 3, 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]
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: [7, 1, 7, 7, 20, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 31, 31, 31, 31, 1, 1, 1, 1, 1] 31
rigid atoms, others: [1, 34, 35, 36, 37, 38, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 70
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040085 none CC(=NNC1=C2C=CSC2=CC=N1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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, 14, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 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, 7, 7, 7, 3, 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]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [23, 23, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 23, 23, 23, 13, 1, 1, 1, 1, 31, 31, 31, 31, 31] 31
rigid atoms, others: [32, 33, 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, 34, 35, 36, 37, 38])
total number of confs: 59
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040085 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040085
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040085/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040085
Building REAL300000040086
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040086'
/scratch/stefan/7769621/working/building/REAL300000040086 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040086

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040086/0 /scratch/stefan/7769621/working/building/REAL300000040086 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 120)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/120
`/scratch/stefan/7769621/working/3D/120' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC(C=NNC3=C4C=CSC4=CC=N3)=CC=C2O1)

`REAL300000040086.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040086.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040086/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040086 none O=C([O-])C1=CC2=CC(C=NNC3=C4C=CSC4=CC=N3)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 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
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [81, 81, 81, 81, 81, 81, 81, 52, 52, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 81, 52, 13, 1, 1, 1, 1, 81, 81] 81
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 33, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 130
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040086 none O=C([O-])C1=CC2=CC(C=NNC3=C4C=CSC4=CC=N3)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 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
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 49, 81, 81, 81, 81, 81, 81, 81, 81, 1, 1, 1, 1, 1, 1, 11, 49, 81, 81, 81, 81, 1, 1] 81
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 33] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31])
total number of confs: 173
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040086 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040086/1 /scratch/stefan/7769621/working/building/REAL300000040086 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 121)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/121
`/scratch/stefan/7769621/working/3D/121' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC(CN=NC3=C4C=CSC4=CC=N3)=CC=C2O1)

`REAL300000040086.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040086.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040086/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040086 none O=C([O-])C1=CC2=CC(CN=NC3=C4C=CSC4=CC=N3)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 12, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
152  conformations in input
total number of sets (complete confs): 152
using faster count positions algorithm for large data
unique positions, atoms: [152, 151, 152, 151, 151, 151, 151, 54, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 151, 151, 151, 151, 151, 151, 54, 54, 1, 1, 1, 1, 151, 151] 152
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 33, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 308
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040086 none O=C([O-])C1=CC2=CC(CN=NC3=C4C=CSC4=CC=N3)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 1, 12, 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, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 70, 70, 151, 151, 151, 151, 151, 151, 151, 151, 1, 1, 1, 1, 1, 1, 8, 8, 151, 151, 151, 151, 1, 1] 152
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 33] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31])
total number of confs: 229
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040086 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040086
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040086/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040086/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040086
Building REAL300000040087
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040087'
/scratch/stefan/7769621/working/building/REAL300000040087 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040087

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040087/0 /scratch/stefan/7769621/working/building/REAL300000040087 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 122)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/122
`/scratch/stefan/7769621/working/3D/122' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2C(C=NNC3=C4C=CSC4=CC=N3)=CC=CN12)

`REAL300000040087.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040087.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040087/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040087 none O=C([O-])C1=CN=C2C(C=NNC3=C4C=CSC4=CC=N3)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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, 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, 7, 7]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 38, 38, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 38, 12, 1, 1, 1, 1, 48, 48, 48] 48
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 33, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 74
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040087 none O=C([O-])C1=CN=C2C(C=NNC3=C4C=CSC4=CC=N3)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 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, 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, 7, 7]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 28, 48, 48, 48, 48, 48, 47, 48, 48, 1, 1, 1, 1, 1, 10, 28, 48, 48, 47, 48, 1, 1, 1] 48
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 20, 21, 22, 23, 24, 33, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30])
total number of confs: 98
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040087 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040087
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040087/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040087
Building REAL300000040088
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040088'
/scratch/stefan/7769621/working/building/REAL300000040088 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040088

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040088/0 /scratch/stefan/7769621/working/building/REAL300000040088 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 123)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/123
`/scratch/stefan/7769621/working/3D/123' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(F)C=CC=C1C=NNC1=C2C=CSC2=CC=N1)

`REAL300000040088.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040088.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040088/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040088 none O=C([O-])C1=C(F)C=CC=C1C=NNC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.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, 15, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 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]
0  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 36, 36, 28, 27, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 27, 11, 1, 1, 1, 1] 36
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26])
total number of confs: 61
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040088 none O=C([O-])C1=C(F)C=CC=C1C=NNC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.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, 15, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 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]
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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 6, 20, 36, 36, 36, 36] 36
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30])
total number of confs: 82
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040088 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040088
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040088/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040088
Building REAL300000040089
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040089'
/scratch/stefan/7769621/working/building/REAL300000040089 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040089

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040089/0 /scratch/stefan/7769621/working/building/REAL300000040089 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 124)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/124
`/scratch/stefan/7769621/working/3D/124' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(COC2=CC=CC=C2CN=NC2=C3C=CSC3=CC=N2)O1)

`REAL300000040089.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040089.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040089/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040089 none O=C([O-])C1=CC=C(COC2=CC=CC=C2CN=NC2=C3C=CSC3=CC=N2)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', '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, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 67, 67, 67, 54, 40, 25, 25, 25, 16, 25, 25, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 54, 54, 25, 24, 25, 25, 11, 11, 1, 1, 1, 1] 67
rigid atoms, others: [38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 213
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: REAL300000040089 none O=C([O-])C1=CC=C(COC2=CC=CC=C2CN=NC2=C3C=CSC3=CC=N2)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', '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, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [37, 37, 37, 37, 37, 37, 15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 37, 37, 37, 15, 15, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25] 67
rigid atoms, others: [32, 33, 34, 35, 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, 36, 37, 38, 39, 40, 41])
total number of confs: 117
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040089 none O=C([O-])C1=CC=C(COC2=CC=CC=C2CN=NC2=C3C=CSC3=CC=N2)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', '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, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 28, 37, 37, 29, 37, 37, 37, 43, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1, 1, 8, 8, 37, 37, 37, 37, 43, 43, 67, 67, 67, 67] 67
rigid atoms, others: [1, 3, 4, 5, 6, 7, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 176
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040089 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040089/1 /scratch/stefan/7769621/working/building/REAL300000040089 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 125)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/125
`/scratch/stefan/7769621/working/3D/125' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=C3C=CSC3=CC=N2)O1)

`REAL300000040089.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040089.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040089/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040089 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=C3C=CSC3=CC=N2)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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', '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, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 150, 68, 31, 31, 31, 31, 31, 31, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 150, 150, 31, 31, 31, 31, 18, 6, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 549
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: REAL300000040089 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=C3C=CSC3=CC=N2)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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', '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, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 8, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 31, 31, 31, 31, 31, 31, 31, 31, 98, 98, 98, 32, 32, 1, 1, 1, 1, 4, 15, 31, 31, 31, 31] 201
rigid atoms, others: [32, 33, 34, 35, 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, 36, 37, 38, 39, 40, 41])
total number of confs: 242
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040089 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=C3C=CSC3=CC=N2)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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', '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, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 43, 98, 98, 98, 98, 98, 98, 127, 127, 150, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 8, 8, 98, 98, 98, 98, 127, 150, 201, 201, 201, 201] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 436
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040089 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040089
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040089/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040089/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040089
Building REAL300000040090
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040090'
/scratch/stefan/7769621/working/building/REAL300000040090 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040090

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040090/0 /scratch/stefan/7769621/working/building/REAL300000040090 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 126)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/126
`/scratch/stefan/7769621/working/3D/126' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Br)C=CC=C1C=NNC1=C2C=CSC2=CC=N1)

`REAL300000040090.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040090.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040090/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040090 none O=C([O-])C1=C(Br)C=CC=C1C=NNC1=C2C=CSC2=CC=N1 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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.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, 17, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 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]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [28, 28, 28, 28, 28, 28, 27, 28, 28, 27, 27, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 28, 28, 27, 11, 1, 1, 1, 1] 28
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26])
total number of confs: 49
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040090 none O=C([O-])C1=C(Br)C=CC=C1C=NNC1=C2C=CSC2=CC=N1 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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.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, 17, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 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]
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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 6, 16, 28, 28, 28, 28] 28
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30])
total number of confs: 62
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040090 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040090
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040090/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040090
Building REAL300000040091
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040091'
/scratch/stefan/7769621/working/building/REAL300000040091 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040091

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040091/0 /scratch/stefan/7769621/working/building/REAL300000040091 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 127)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/127
`/scratch/stefan/7769621/working/3D/127' -> `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=NNC1=C2C=CSC2=CC=N1)

`REAL300000040091.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040091.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040091/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040091 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NNC1=C2C=CSC2=CC=N1 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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 65, 65, 65, 65, 65, 73, 65, 65, 65, 65, 65, 65, 65, 65, 35, 35, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 73, 73, 73, 65, 73, 73, 73, 65, 65, 35, 11, 1, 1, 1, 1] 73
rigid atoms, others: [39, 40, 41, 42, 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])
total number of confs: 133
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040091 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NNC1=C2C=CSC2=CC=N1 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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 7, 29, 65, 65, 65, 65, 65, 65, 65, 65, 3, 3, 3, 1, 3, 3, 3, 1, 1, 7, 29, 65, 65, 65, 65] 73
rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 15, 16, 35, 36, 31] set([0, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 37, 38, 39, 40, 41, 42])
total number of confs: 129
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040091 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040091/1 /scratch/stefan/7769621/working/building/REAL300000040091 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 128)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/128
`/scratch/stefan/7769621/working/3D/128' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2CN=NC1=C2C=CSC2=CC=N1)

`REAL300000040091.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040091.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040091/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040091 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2CN=NC1=C2C=CSC2=CC=N1 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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [170, 107, 107, 107, 107, 107, 178, 107, 107, 107, 107, 107, 107, 134, 134, 61, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 170, 170, 170, 107, 179, 179, 179, 107, 107, 61, 61, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 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])
total number of confs: 636
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040091 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2CN=NC1=C2C=CSC2=CC=N1 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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 4, 36, 36, 107, 107, 107, 107, 107, 107, 107, 107, 2, 2, 2, 1, 4, 4, 4, 1, 1, 4, 4, 107, 107, 107, 107] 201
rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 15, 16, 35, 36, 31] set([0, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 37, 38, 39, 40, 41, 42])
total number of confs: 169
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040091 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040091
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040091/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040091/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040091
Building REAL300000040092
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040092'
/scratch/stefan/7769621/working/building/REAL300000040092 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040092

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040092/0 /scratch/stefan/7769621/working/building/REAL300000040092 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 129)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/129
`/scratch/stefan/7769621/working/3D/129' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2OCOC2=C1C=NNC1=C2C=CSC2=CC=N1)

`REAL300000040092.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040092.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040092/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040092 none O=C([O-])C1=CC=C2OCOC2=C1C=NNC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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, 12, 5, 12, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 53, 53, 53, 53, 53, 39, 39, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 39, 12, 1, 1, 1, 1] 53
rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29])
total number of confs: 83
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040092 none O=C([O-])C1=CC=C2OCOC2=C1C=NNC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', '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, 12, 5, 12, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 29, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 6, 29, 53, 53, 53, 53] 53
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27] set([0, 32, 2, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31])
total number of confs: 113
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040092 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040092
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040092/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040092
Building REAL300000040093
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040093'
/scratch/stefan/7769621/working/building/REAL300000040093 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040093

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040093/0 /scratch/stefan/7769621/working/building/REAL300000040093 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 130)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/130
`/scratch/stefan/7769621/working/3D/130' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=CC=C(C(=O)[O-])C(C=NNC2=C3C=CSC3=CC=N2)=C1)

`REAL300000040093.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040093.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040093/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040093 none N#CC1=CC=C(C(=O)[O-])C(C=NNC2=C3C=CSC3=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [52, 52, 52, 52, 52, 52, 52, 52, 52, 36, 36, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 36, 11, 1, 1, 1, 1, 52] 52
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 31])
total number of confs: 87
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040093 none N#CC1=CC=C(C(=O)[O-])C(C=NNC2=C3C=CSC3=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 6, 6, 30, 52, 52, 52, 52, 52, 52, 52, 52, 1, 1, 1, 6, 30, 52, 52, 52, 52, 1] 52
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 22, 23, 24, 31] set([7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30])
total number of confs: 112
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040093 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040093
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040093/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040093
Building REAL300000040094
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040094'
/scratch/stefan/7769621/working/building/REAL300000040094 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040094

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040094/0 /scratch/stefan/7769621/working/building/REAL300000040094 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 131)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/131
`/scratch/stefan/7769621/working/3D/131' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC2=C3C=CSC3=CC=N2)C=C1Cl)

`REAL300000040094.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040094.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040094/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040094 none O=C([O-])COC1=CC=C(C=NNC2=C3C=CSC3=CC=N2)C=C1Cl 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.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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, 14, 1, 1, 1, 8, 1, 1, 16, 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, 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, 164, 69, 67, 69, 69, 29, 29, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 201, 201, 69, 69, 29, 8, 1, 1, 1, 1, 69] 201
rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 429
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040094 none O=C([O-])COC1=CC=C(C=NNC2=C3C=CSC3=CC=N2)C=C1Cl 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.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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, 14, 1, 1, 1, 8, 1, 1, 16, 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, 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: [49, 28, 49, 7, 1, 1, 1, 1, 1, 1, 6, 6, 30, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1, 1, 28, 28, 1, 1, 6, 30, 69, 69, 69, 69, 1] 201
rigid atoms, others: [34, 4, 5, 6, 7, 8, 9, 21, 22, 23, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 292
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040094 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040094/1 /scratch/stefan/7769621/working/building/REAL300000040094 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 132)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/132
`/scratch/stefan/7769621/working/3D/132' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(CN=NC2=C3C=CSC3=CC=N2)C=C1Cl)

`REAL300000040094.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040094.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040094/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040094 none O=C([O-])COC1=CC=C(CN=NC2=C3C=CSC3=CC=N2)C=C1Cl 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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 16, 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, 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, 193, 63, 63, 64, 64, 14, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 64, 64, 64, 201, 201, 64, 64, 14, 14, 1, 1, 1, 1, 64] 201
rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 346
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040094 none O=C([O-])COC1=CC=C(CN=NC2=C3C=CSC3=CC=N2)C=C1Cl 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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 16, 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, 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: [19, 15, 19, 5, 1, 1, 1, 1, 1, 1, 8, 60, 60, 64, 64, 64, 64, 64, 64, 64, 64, 1, 1, 1, 15, 15, 1, 1, 8, 8, 64, 64, 64, 64, 1] 201
rigid atoms, others: [34, 4, 5, 6, 7, 8, 9, 21, 22, 23, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 155
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040094 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040094
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040094/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040094/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040094
Building REAL300000040095
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040095'
/scratch/stefan/7769621/working/building/REAL300000040095 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040095

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040095/0 /scratch/stefan/7769621/working/building/REAL300000040095 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 133)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/133
`/scratch/stefan/7769621/working/3D/133' -> `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=NNC2=C3C=CSC3=CC=N2)C=C1)

`REAL300000040095.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040095.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040095/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040095 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC2=C3C=CSC3=CC=N2)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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 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, 7, 7, 7, 7]
0  hydrogens need rotated
111  conformations in input
total number of sets (complete confs): 111
using faster count positions algorithm for large data
unique positions, atoms: [111, 111, 111, 99, 63, 32, 63, 63, 18, 62, 62, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 62, 62, 111, 111, 99, 62, 62, 18, 6, 1, 1, 1, 1, 62, 62] 111
rigid atoms, others: [33, 34, 35, 36, 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, 37, 38])
total number of confs: 552
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040095 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC2=C3C=CSC3=CC=N2)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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 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, 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: [9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 30, 62, 62, 62, 62, 62, 62, 62, 62, 1, 1, 9, 9, 5, 1, 1, 6, 30, 62, 62, 62, 62, 1, 1] 111
rigid atoms, others: [5, 38, 8, 9, 10, 11, 12, 24, 25, 29, 30, 37] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36])
total number of confs: 157
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040095 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040095
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040095/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040095
Building REAL300000040096
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040096'
/scratch/stefan/7769621/working/building/REAL300000040096 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040096

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040096/0 /scratch/stefan/7769621/working/building/REAL300000040096 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 134)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/134
`/scratch/stefan/7769621/working/3D/134' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NSC(C=NNC2=C3C=CSC3=CC=N2)=C1C(=O)[O-])

`REAL300000040096.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040096.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040096/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040096 none CC1=NSC(C=NNC2=C3C=CSC3=CC=N2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 11, 11, 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, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [47, 47, 47, 47, 36, 36, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47, 36, 12, 1, 1, 1, 1] 47
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25])
total number of confs: 78
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040096 none CC1=NSC(C=NNC2=C3C=CSC3=CC=N2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 1, 11, 11, 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, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 26, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 3, 3, 2, 2, 2, 6, 26, 47, 47, 47, 47] 47
rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 99
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040096 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040096
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040096/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040096
Building REAL300000040097
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040097'
/scratch/stefan/7769621/working/building/REAL300000040097 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040097

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040097/0 /scratch/stefan/7769621/working/building/REAL300000040097 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 135)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/135
`/scratch/stefan/7769621/working/3D/135' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=C(C=NNC3=C4C=CSC4=CC=N3)C(F)=CC=C2S1)

`REAL300000040097.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040097.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040097/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040097 none O=C([O-])C1=CC2=C(C=NNC3=C4C=CSC4=CC=N3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7]
0  hydrogens need rotated
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [91, 91, 91, 91, 91, 91, 47, 47, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 91, 91, 91, 91, 91, 91, 91, 47, 11, 1, 1, 1, 1, 91, 91] 91
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 33, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 136
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040097 none O=C([O-])C1=CC2=C(C=NNC3=C4C=CSC4=CC=N3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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, 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: [2, 1, 2, 1, 1, 1, 1, 1, 11, 11, 56, 91, 91, 91, 91, 91, 90, 91, 91, 1, 1, 1, 1, 1, 1, 1, 11, 56, 91, 91, 90, 91, 1, 1] 91
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31])
total number of confs: 192
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040097 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040097
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040097/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040097
Building REAL300000040098
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040098'
/scratch/stefan/7769621/working/building/REAL300000040098 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040098

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040098/0 /scratch/stefan/7769621/working/building/REAL300000040098 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 136)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/136
`/scratch/stefan/7769621/working/3D/136' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=NNC1=C2C=CSC2=CC=N1)

`REAL300000040098.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040098.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040098/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040098 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 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, 7]
0  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 44, 44, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 66, 44, 12, 1, 1, 1, 1] 66
rigid atoms, others: [32, 33, 34, 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: 99
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040098 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 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, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 30, 66, 66, 66, 66, 66, 66, 66, 66, 3, 3, 3, 1, 1, 1, 12, 30, 66, 66, 66, 66] 66
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 32, 34, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31])
total number of confs: 127
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040098 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040098/1 /scratch/stefan/7769621/working/building/REAL300000040098 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 137)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/137
`/scratch/stefan/7769621/working/3D/137' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(=O)[O-])=CC=C1CN=NC1=C2C=CSC2=CC=N1)

`REAL300000040098.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040098.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040098/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040098 none COC1=CC(C(=O)[O-])=CC=C1CN=NC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 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
184  conformations in input
total number of sets (complete confs): 184
using faster count positions algorithm for large data
unique positions, atoms: [184, 184, 184, 184, 182, 184, 184, 184, 184, 184, 64, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 184, 184, 184, 184, 184, 184, 64, 64, 1, 1, 1, 1] 184
rigid atoms, others: [32, 33, 34, 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: 373
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040098 none COC1=CC(C(=O)[O-])=CC=C1CN=NC1=C2C=CSC2=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 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
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, 1, 1, 1, 1, 1, 1, 8, 61, 62, 184, 184, 184, 184, 184, 184, 184, 184, 3, 3, 3, 1, 1, 1, 8, 8, 184, 184, 184, 184] 184
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 32, 34, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31])
total number of confs: 270
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040098 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040098
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040098/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040098/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040098
Building REAL300000040099
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040099'
/scratch/stefan/7769621/working/building/REAL300000040099 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040099

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040099/0 /scratch/stefan/7769621/working/building/REAL300000040099 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 138)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/138
`/scratch/stefan/7769621/working/3D/138' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=C4C=CSC4=CC=N3)=N2)C1)

`REAL300000040099.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040099.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040099/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040099 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=C4C=CSC4=CC=N3)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
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, 69, 201, 69, 69, 69, 49, 49, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69, 201, 201, 201, 69, 69, 49, 10, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [32, 33, 34, 35, 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, 36, 37])
total number of confs: 466
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: REAL300000040099 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=C4C=CSC4=CC=N3)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens 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, 13, 25, 13, 13, 13, 1, 13, 1, 1, 1, 1, 1, 5, 5, 19, 69, 69, 69, 69, 69, 69, 69, 69, 1, 13, 13, 13, 1, 1, 5, 19, 69, 69, 69, 69, 13, 13] 201
rigid atoms, others: [6, 8, 9, 10, 11, 12, 24, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 183
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040099 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=C4C=CSC4=CC=N3)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens 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, 13, 13, 13, 13, 37, 37, 113, 201, 201, 201, 201, 201, 201, 201, 201, 13, 1, 1, 1, 13, 13, 37, 113, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 25, 26, 27, 37, 36] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 422
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040099 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040099/1 /scratch/stefan/7769621/working/building/REAL300000040099 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 139)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/139
`/scratch/stefan/7769621/working/3D/139' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])[C@H]1C[C@H](N2C=CC(CN=NC3=C4C=CSC4=CC=N3)=N2)C1)

`REAL300000040099.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040099.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040099/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040099 none O=C([O-])[C@H]1C[C@H](N2C=CC(CN=NC3=C4C=CSC4=CC=N3)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 5, 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, 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, 54, 201, 54, 54, 54, 17, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 201, 201, 201, 54, 54, 17, 17, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [32, 33, 34, 35, 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, 36, 37])
total number of confs: 483
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: REAL300000040099 none O=C([O-])[C@H]1C[C@H](N2C=CC(CN=NC3=C4C=CSC4=CC=N3)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 5, 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, 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: [19, 11, 19, 11, 11, 11, 1, 11, 1, 1, 1, 1, 1, 7, 47, 47, 54, 54, 54, 54, 54, 54, 54, 54, 1, 11, 11, 11, 1, 1, 7, 7, 54, 54, 54, 54, 11, 11] 201
rigid atoms, others: [6, 8, 9, 10, 11, 12, 24, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 135
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040099 none O=C([O-])[C@H]1C[C@H](N2C=CC(CN=NC3=C4C=CSC4=CC=N3)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 5, 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, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 45, 193, 193, 201, 201, 201, 201, 201, 201, 201, 201, 11, 1, 1, 1, 11, 11, 45, 45, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 25, 26, 27, 37, 36] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 344
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040099 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040099
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040099/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040099/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040099
Building REAL300000040100
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040100'
/scratch/stefan/7769621/working/building/REAL300000040100 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040100

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040100/0 /scratch/stefan/7769621/working/building/REAL300000040100 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 140)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/140
`/scratch/stefan/7769621/working/3D/140' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=CC=C1CN=NC1=NC=CC=C1Cl)

`REAL300000040100.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040100.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040100/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040100 none O=C([O-])COC1=CC=CC=C1CN=NC1=NC=CC=C1Cl 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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 135, 40, 40, 40, 14, 40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 40, 40, 40, 40, 9, 9, 1, 1, 1] 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, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 623
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040100 none O=C([O-])COC1=CC=CC=C1CN=NC1=NC=CC=C1Cl 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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 34, 61, 8, 1, 1, 1, 1, 1, 1, 1, 1, 6, 40, 40, 40, 40, 40, 40, 40, 40, 34, 34, 1, 1, 1, 1, 6, 6, 40, 40, 40] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 252
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040100 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040100
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040100/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040100
Building REAL300000040101
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040101'
/scratch/stefan/7769621/working/building/REAL300000040101 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040101

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040101/0 /scratch/stefan/7769621/working/building/REAL300000040101 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 141)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/141
`/scratch/stefan/7769621/working/3D/141' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=NC=CC=C1Cl)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1)

`REAL300000040101.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040101.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040101/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040101 none CC(N=NC1=NC=CC=C1Cl)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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]
dock color type numbers: [7, 7, 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]
0  hydrogens need rotated
160  conformations in input
total number of sets (complete confs): 160
using faster count positions algorithm for large data
unique positions, atoms: [17, 1, 18, 135, 135, 160, 160, 160, 160, 160, 160, 1, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 21, 19, 22, 17, 160, 160, 160, 12, 12, 1, 1, 12, 12] 160
rigid atoms, others: [34, 35, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37])
total number of confs: 291
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: REAL300000040101 none CC(N=NC1=NC=CC=C1Cl)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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]
dock color type numbers: [7, 7, 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]
0  hydrogens need rotated
160  conformations in input
total number of sets (complete confs): 160
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 49, 49, 90, 90, 90, 90, 90, 90, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 7, 7, 7, 7, 90, 90, 90, 1, 1, 12, 12, 1, 1] 160
rigid atoms, others: [32, 1, 36, 37, 33, 11, 12, 13, 14, 15, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 150
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040101 none CC(N=NC1=NC=CC=C1Cl)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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]
dock color type numbers: [7, 7, 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]
0  hydrogens need rotated
160  conformations in input
total number of sets (complete confs): 160
using faster count positions algorithm for large data
unique positions, atoms: [43, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 43, 90, 90, 55, 56, 160, 160, 160, 160, 160, 160, 160, 90, 90, 43, 43, 43, 43, 1, 1, 1, 90, 90, 160, 160, 90, 90] 160
rigid atoms, others: [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, 32, 33, 34, 35, 36, 37])
total number of confs: 433
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040101 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040101/1 /scratch/stefan/7769621/working/building/REAL300000040101 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 142)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/142
`/scratch/stefan/7769621/working/3D/142' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NC=CC=C1Cl)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1)

`REAL300000040101.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040101.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040101/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040101 none CC(=NNC1=NC=CC=C1Cl)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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 1, 1, 16, 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, 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]
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: [15, 1, 15, 26, 113, 172, 172, 172, 172, 172, 172, 1, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 15, 23, 21, 113, 172, 172, 172, 12, 12, 1, 1, 12, 12] 172
rigid atoms, others: [34, 35, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37])
total number of confs: 426
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: REAL300000040101 none CC(=NNC1=NC=CC=C1Cl)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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 1, 1, 16, 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, 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]
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: [6, 1, 6, 6, 35, 112, 112, 112, 112, 112, 112, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 6, 6, 6, 35, 112, 112, 112, 1, 1, 12, 12, 1, 1] 172
rigid atoms, others: [32, 1, 36, 37, 33, 11, 12, 13, 14, 15, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 197
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040101 none CC(=NNC1=NC=CC=C1Cl)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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 1, 1, 16, 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, 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]
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: [50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 50, 112, 112, 83, 83, 172, 172, 172, 172, 172, 172, 172, 112, 112, 51, 51, 51, 11, 1, 1, 1, 112, 112, 172, 172, 112, 112] 172
rigid atoms, others: [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, 32, 33, 34, 35, 36, 37])
total number of confs: 397
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040101 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040101
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040101/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040101/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040101
Building REAL300000040102
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040102'
/scratch/stefan/7769621/working/building/REAL300000040102 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040102

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040102/0 /scratch/stefan/7769621/working/building/REAL300000040102 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 143)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/143
`/scratch/stefan/7769621/working/3D/143' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(CN=NC2=NC=CC=C2Cl)=CC=C1OCC(=O)[O-])

`REAL300000040102.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040102.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040102/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040102 none COC1=CC(CN=NC2=NC=CC=C2Cl)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 11, 11, 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, 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]
0  hydrogens 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, 47, 47, 47, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 133, 199, 201, 201, 87, 87, 87, 47, 9, 9, 1, 1, 1, 47, 47, 199, 199] 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])
total number of confs: 641
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040102 none COC1=CC(CN=NC2=NC=CC=C2Cl)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 11, 11, 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, 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]
0  hydrogens 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, 46, 46, 46, 46, 46, 46, 46, 47, 1, 1, 1, 1, 9, 23, 30, 30, 3, 3, 3, 1, 6, 6, 46, 46, 47, 1, 1, 23, 23] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 33, 15, 16, 17, 18, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 161
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040102 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040102/1 /scratch/stefan/7769621/working/building/REAL300000040102 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 144)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/144
`/scratch/stefan/7769621/working/3D/144' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=NC=CC=C2Cl)=CC=C1OCC(=O)[O-])

`REAL300000040102.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040102.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040102/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040102 none COC1=CC(C=NNC2=NC=CC=C2Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 1, 1, 16, 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, 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]
0  hydrogens 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, 42, 42, 42, 18, 17, 3, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 138, 201, 201, 201, 82, 82, 82, 42, 17, 3, 1, 1, 1, 42, 42, 201, 201] 201
rigid atoms, others: [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, 32, 33, 34, 35])
total number of confs: 573
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040102 none COC1=CC(C=NNC2=NC=CC=C2Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 1, 1, 16, 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, 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]
0  hydrogens 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, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 9, 37, 61, 61, 4, 4, 4, 1, 7, 21, 42, 42, 42, 1, 1, 37, 37] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 33, 15, 16, 17, 18, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 301
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040102 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040102
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040102/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040102/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040102
Building REAL300000040103
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040103'
/scratch/stefan/7769621/working/building/REAL300000040103 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040103

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040103/0 /scratch/stefan/7769621/working/building/REAL300000040103 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 145)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/145
`/scratch/stefan/7769621/working/3D/145' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(CN=NC2=NC=CC=C2Cl)C=C1)

`REAL300000040103.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040103.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040103/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040103 none O=C([O-])COC1=CC=C(CN=NC2=NC=CC=C2Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.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']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 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, 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, 149, 65, 22, 86, 86, 21, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 86, 86, 201, 201, 86, 86, 21, 21, 1, 1, 1, 86, 86] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 718
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040103 none O=C([O-])COC1=CC=C(CN=NC2=NC=CC=C2Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.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']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 11, 23, 3, 1, 1, 1, 1, 1, 1, 8, 63, 63, 85, 85, 85, 85, 85, 86, 1, 1, 11, 11, 1, 1, 8, 8, 85, 85, 86, 1, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 19, 20, 23, 24, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 25, 26, 27, 28, 29])
total number of confs: 206
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040103 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040103
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040103/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040103
Building REAL300000040104
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040104'
/scratch/stefan/7769621/working/building/REAL300000040104 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040104

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040104/0 /scratch/stefan/7769621/working/building/REAL300000040104 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 146)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/146
`/scratch/stefan/7769621/working/3D/146' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=NC=CC=C1Cl)C1=CC=CC(OCC(=O)[O-])=C1)

`REAL300000040104.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040104.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040104/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040104 none CC(N=NC1=NC=CC=C1Cl)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 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, 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: [8, 1, 8, 41, 41, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 6, 22, 35, 35, 1, 8, 8, 8, 8, 50, 50, 50, 1, 1, 1, 23, 23, 1] 201
rigid atoms, others: [1, 34, 11, 12, 13, 14, 15, 16, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33])
total number of confs: 195
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040104 none CC(N=NC1=NC=CC=C1Cl)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 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, 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: [16, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 144, 201, 201, 201, 50, 16, 16, 16, 16, 1, 1, 1, 50, 50, 50, 201, 201, 50] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34])
total number of confs: 540
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040104 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040104/1 /scratch/stefan/7769621/working/building/REAL300000040104 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 147)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/147
`/scratch/stefan/7769621/working/3D/147' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NC=CC=C1Cl)C1=CC=CC(OCC(=O)[O-])=C1)

`REAL300000040104.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040104.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040104/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040104 none CC(=NNC1=NC=CC=C1Cl)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 1, 1, 16, 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, 3, 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]
0  hydrogens 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, 30, 60, 60, 60, 60, 60, 60, 1, 1, 1, 1, 1, 1, 6, 22, 37, 37, 1, 9, 9, 9, 30, 60, 60, 60, 1, 1, 1, 22, 22, 1] 201
rigid atoms, others: [1, 34, 11, 12, 13, 14, 15, 16, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33])
total number of confs: 239
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040104 none CC(=NNC1=NC=CC=C1Cl)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 1, 1, 16, 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, 3, 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]
0  hydrogens 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, 23, 6, 1, 1, 1, 1, 1, 1, 1, 1, 23, 60, 60, 60, 60, 60, 133, 201, 201, 201, 60, 23, 23, 23, 6, 1, 1, 1, 60, 60, 60, 201, 201, 60] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34])
total number of confs: 559
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040104 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040104
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040104/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040104/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040104
Building REAL300000040105
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040105'
/scratch/stefan/7769621/working/building/REAL300000040105 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040105

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040105/0 /scratch/stefan/7769621/working/building/REAL300000040105 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 148)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/148
`/scratch/stefan/7769621/working/3D/148' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=NC=CC=C1Cl)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1)

`REAL300000040105.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040105.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040105/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040105 none CC(N=NC1=NC=CC=C1Cl)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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]
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: [5, 1, 5, 23, 23, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 1, 1, 5, 5, 5, 5, 37, 37, 37, 1, 1, 9, 14, 14, 1, 1] 107
rigid atoms, others: [32, 1, 37, 38, 33, 11, 12, 13, 14, 15, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36])
total number of confs: 118
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040105 none CC(N=NC1=NC=CC=C1Cl)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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]
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: [19, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 19, 37, 37, 19, 19, 62, 62, 62, 105, 107, 107, 107, 37, 37, 19, 19, 19, 19, 1, 1, 1, 37, 37, 105, 107, 107, 37, 37] 107
rigid atoms, others: [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, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 479
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040105 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040105/1 /scratch/stefan/7769621/working/building/REAL300000040105 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 149)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/149
`/scratch/stefan/7769621/working/3D/149' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NC=CC=C1Cl)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1)

`REAL300000040105.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040105.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040105/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040105 none CC(=NNC1=NC=CC=C1Cl)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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 1, 1, 16, 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, 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]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 26, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 1, 1, 6, 6, 6, 26, 43, 43, 43, 1, 1, 9, 17, 17, 1, 1] 113
rigid atoms, others: [32, 1, 37, 38, 33, 11, 12, 13, 14, 15, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36])
total number of confs: 163
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040105 none CC(=NNC1=NC=CC=C1Cl)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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 1, 1, 16, 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, 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]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 3, 1, 1, 1, 1, 1, 1, 1, 1, 18, 43, 43, 30, 43, 66, 66, 66, 107, 113, 113, 113, 43, 43, 18, 18, 18, 3, 1, 1, 1, 43, 43, 107, 113, 113, 43, 43] 113
rigid atoms, others: [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, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 450
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040105 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040105
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040105/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040105/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040105
Building REAL300000040106
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040106'
/scratch/stefan/7769621/working/building/REAL300000040106 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040106

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040106/0 /scratch/stefan/7769621/working/building/REAL300000040106 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 150)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/150
`/scratch/stefan/7769621/working/3D/150' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=NC=CC=C1Cl)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1)

`REAL300000040106.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040106.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040106/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040106 none CC(N=NC1=NC=CC=C1Cl)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 11, 11, 1, 1, 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, 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]
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: [4, 1, 4, 20, 20, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 1, 1, 4, 4, 4, 4, 23, 23, 23, 1, 1, 9, 9, 9, 9, 9, 1, 1] 64
rigid atoms, others: [1, 34, 33, 40, 41, 11, 12, 13, 14, 15, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39])
total number of confs: 62
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040106 none CC(N=NC1=NC=CC=C1Cl)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 11, 11, 1, 1, 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, 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]
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: [12, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 12, 23, 23, 12, 12, 37, 37, 37, 64, 64, 64, 64, 64, 23, 23, 12, 12, 12, 12, 1, 1, 1, 23, 23, 64, 64, 64, 64, 64, 23, 23] 64
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 273
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040106 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040106/1 /scratch/stefan/7769621/working/building/REAL300000040106 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 151)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/151
`/scratch/stefan/7769621/working/3D/151' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NC=CC=C1Cl)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1)

`REAL300000040106.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040106.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040106/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040106 none CC(=NNC1=NC=CC=C1Cl)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 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]
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: [5, 1, 5, 5, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 1, 1, 5, 5, 5, 21, 21, 21, 21, 1, 1, 9, 9, 9, 9, 9, 1, 1] 55
rigid atoms, others: [1, 34, 33, 40, 41, 11, 12, 13, 14, 15, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39])
total number of confs: 75
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040106 none CC(=NNC1=NC=CC=C1Cl)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 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]
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: [13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 1, 14, 21, 21, 17, 21, 31, 31, 31, 55, 55, 55, 55, 55, 21, 21, 14, 14, 14, 3, 1, 1, 1, 21, 21, 55, 55, 55, 55, 55, 21, 21] 55
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 192
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040106 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040106
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040106/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040106/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040106
Building REAL300000040107
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040107'
/scratch/stefan/7769621/working/building/REAL300000040107 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040107

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040107/0 /scratch/stefan/7769621/working/building/REAL300000040107 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 152)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/152
`/scratch/stefan/7769621/working/3D/152' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=NC=CC=C1Cl)C1=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C1)

`REAL300000040107.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040107.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040107/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040107 none CC(N=NC1=NC=CC=C1Cl)C1=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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]
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: [3, 1, 3, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 1, 1, 3, 3, 3, 3, 6, 6, 6, 1, 1, 5, 5, 5, 5, 1, 1] 9
rigid atoms, others: [1, 34, 35, 40, 41, 11, 12, 13, 14, 15, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39])
total number of confs: 31
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040107 none CC(N=NC1=NC=CC=C1Cl)C1=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 6, 6, 4, 5, 7, 7, 7, 9, 9, 9, 9, 9, 9, 6, 6, 4, 4, 4, 4, 1, 1, 1, 6, 6, 9, 9, 9, 9, 6, 6] 9
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 33, 31] set([0, 11, 12, 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: 45
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040107 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040107/1 /scratch/stefan/7769621/working/building/REAL300000040107 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 153)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/153
`/scratch/stefan/7769621/working/3D/153' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NC=CC=C1Cl)C1=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C1)

`REAL300000040107.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040107.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040107/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040107 none CC(=NNC1=NC=CC=C1Cl)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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 14, 11, 11, 8, 5, 7, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 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]
0  hydrogens need rotated
4  conformations in input
total number of sets (complete confs): 4
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 4, 4, 4, 4, 1, 1] 4
rigid atoms, others: [1, 34, 35, 40, 41, 11, 12, 13, 14, 15, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39])
total number of confs: 21
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040107 none CC(=NNC1=NC=CC=C1Cl)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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 14, 11, 11, 8, 5, 7, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 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]
0  hydrogens need rotated
4  conformations in input
total number of sets (complete confs): 4
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 3, 3, 2, 2, 2, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 3, 3] 4
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 33, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 21
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040107 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040107
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040107/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040107/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040107
Building REAL300000040108
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040108'
/scratch/stefan/7769621/working/building/REAL300000040108 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040108

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040108/0 /scratch/stefan/7769621/working/building/REAL300000040108 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 154)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/154
`/scratch/stefan/7769621/working/3D/154' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=NC=CC=C1Cl)C1=CC=C(CC(=O)[O-])C=C1)

`REAL300000040108.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040108.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040108/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040108 none CC(N=NC1=NC=CC=C1Cl)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 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, 7, 7, 2, 2, 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: [7, 1, 7, 40, 40, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 7, 7, 7, 7, 51, 51, 51, 1, 1, 2, 2, 1, 1] 81
rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 19, 20, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 101
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040108 none CC(N=NC1=NC=CC=C1Cl)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [29, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 29, 51, 51, 29, 29, 81, 81, 81, 51, 51, 29, 29, 29, 29, 1, 1, 1, 51, 51, 81, 81, 51, 51] 81
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33])
total number of confs: 391
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040108 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040108
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040108/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040108
Building REAL300000040109
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040109'
/scratch/stefan/7769621/working/building/REAL300000040109 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040109

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040109/0 /scratch/stefan/7769621/working/building/REAL300000040109 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 155)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/155
`/scratch/stefan/7769621/working/3D/155' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])OC2=C1C(=NNC1=NC=CC=C1Cl)CCC2)

`REAL300000040109.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040109.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040109/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040109 none CC1=C(C(=O)[O-])OC2=C1C(=NNC1=NC=CC=C1Cl)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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 5, 5, 5, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 34, 33, 33, 11, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 34, 34, 34, 11, 1, 1, 1, 33, 33, 33, 33, 33, 33] 34
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34])
total number of confs: 56
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040109 none CC1=C(C(=O)[O-])OC2=C1C(=NNC1=NC=CC=C1Cl)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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 5, 5, 5, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 9, 33, 33, 33, 33, 33, 33, 1, 1, 1, 2, 2, 2, 9, 33, 33, 33, 1, 1, 1, 1, 1, 1] 34
rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 11, 34, 19, 20, 21, 29, 30, 31] set([4, 5, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 60
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040109 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040109/1 /scratch/stefan/7769621/working/building/REAL300000040109 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 156)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/156
`/scratch/stefan/7769621/working/3D/156' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])OC2=C1C(N=NC1=NC=CC=C1Cl)CCC2)

`REAL300000040109.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040109.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040109/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040109 none CC1=C(C(=O)[O-])OC2=C1C(N=NC1=NC=CC=C1Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 5, 5, 5, 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, 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
16  conformations in input
total number of sets (complete confs): 16
using default count positions algorithm for smaller data
unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 16, 16, 16, 16, 16, 16] 16
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34])
total number of confs: 35
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040109 none CC1=C(C(=O)[O-])OC2=C1C(N=NC1=NC=CC=C1Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 5, 5, 5, 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, 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
16  conformations in input
total number of sets (complete confs): 16
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 8, 8, 16, 16, 16, 16, 16, 16, 1, 1, 1, 2, 2, 2, 1, 16, 16, 16, 1, 1, 1, 1, 1, 1] 16
rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 34, 19, 20, 21, 25, 29, 30, 31] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28])
total number of confs: 35
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040109 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040109
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040109/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040109/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040109
Building REAL300000040110
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040110'
/scratch/stefan/7769621/working/building/REAL300000040110 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040110

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040110/0 /scratch/stefan/7769621/working/building/REAL300000040110 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 157)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/157
`/scratch/stefan/7769621/working/3D/157' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=C(CN=NC2=NC=CC=C2Cl)C=C1)

`REAL300000040110.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040110.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040110/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040110 none O=C([O-])CCOC1=CC=C(CN=NC2=NC=CC=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.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']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 163, 64, 23, 87, 87, 22, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 87, 87, 201, 201, 201, 201, 87, 87, 22, 22, 1, 1, 1, 87, 87] 201
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 660
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040110 none O=C([O-])CCOC1=CC=C(CN=NC2=NC=CC=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.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']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 12, 17, 11, 3, 1, 1, 1, 1, 1, 1, 8, 70, 70, 86, 86, 86, 86, 86, 87, 1, 1, 11, 11, 11, 11, 1, 1, 8, 8, 86, 86, 87, 1, 1] 201
rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 20, 21, 26, 27] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 28, 29, 30, 31, 32])
total number of confs: 190
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040110 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040110
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040110/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040110
Building REAL300000040111
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040111'
/scratch/stefan/7769621/working/building/REAL300000040111 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040111

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040111/0 /scratch/stefan/7769621/working/building/REAL300000040111 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 158)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/158
`/scratch/stefan/7769621/working/3D/158' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(Br)C=C1CN=NC1=NC=CC=C1Cl)

`REAL300000040111.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040111.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040111/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040111 none O=C([O-])COC1=CC=C(Br)C=C1CN=NC1=NC=CC=C1Cl 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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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, 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, 127, 42, 42, 42, 12, 42, 42, 42, 11, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 42, 42, 42, 11, 11, 1, 1, 1] 201
rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 677
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040111 none O=C([O-])COC1=CC=C(Br)C=C1CN=NC1=NC=CC=C1Cl 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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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, 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: [54, 31, 54, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 39, 40, 42, 42, 42, 42, 42, 42, 31, 31, 1, 1, 1, 6, 6, 42, 42, 42] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31])
total number of confs: 237
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040111 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040111/1 /scratch/stefan/7769621/working/building/REAL300000040111 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 159)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/159
`/scratch/stefan/7769621/working/3D/159' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(Br)C=C1C=NNC1=NC=CC=C1Cl)

`REAL300000040111.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040111.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040111/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040111 none O=C([O-])COC1=CC=C(Br)C=C1C=NNC1=NC=CC=C1Cl 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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 8, 1, 1, 1, 1, 16, 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, 7, 4, 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, 159, 63, 63, 63, 36, 63, 63, 63, 35, 35, 7, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 63, 63, 63, 35, 7, 1, 1, 1] 201
rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 579
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040111 none O=C([O-])COC1=CC=C(Br)C=C1C=NNC1=NC=CC=C1Cl 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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 8, 1, 1, 1, 1, 16, 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, 7, 4, 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: [72, 38, 72, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 27, 63, 63, 63, 63, 63, 63, 38, 38, 1, 1, 1, 4, 27, 63, 63, 63] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31])
total number of confs: 349
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040111 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040111
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040111/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040111/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040111
Building REAL300000040112
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040112'
/scratch/stefan/7769621/working/building/REAL300000040112 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040112

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040112/0 /scratch/stefan/7769621/working/building/REAL300000040112 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 160)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/160
`/scratch/stefan/7769621/working/3D/160' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=CC(CN=NC2=NC=CC=C2Cl)=C1)C(=O)[O-])

`REAL300000040112.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040112.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040112/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040112 none CC(OC1=CC=CC(CN=NC2=NC=CC=C2Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'N.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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 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, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 168, 53, 53, 53, 53, 53, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 201, 201, 201, 201, 201, 201, 201, 53, 53, 53, 9, 9, 1, 1, 1, 53] 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])
total number of confs: 434
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040112 none CC(OC1=CC=CC(CN=NC2=NC=CC=C2Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'N.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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 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, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 8, 1, 1, 1, 1, 1, 1, 1, 8, 53, 53, 53, 53, 53, 53, 53, 53, 1, 19, 27, 27, 19, 19, 19, 19, 1, 1, 1, 8, 8, 53, 53, 53, 1] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 34, 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])
total number of confs: 168
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040112 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040112
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040112/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040112
Building REAL300000040113
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040113'
/scratch/stefan/7769621/working/building/REAL300000040113 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040113

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040113/0 /scratch/stefan/7769621/working/building/REAL300000040113 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 161)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/161
`/scratch/stefan/7769621/working/3D/161' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=CC(CN=NC2=NC=CC=C2Cl)=C1)

`REAL300000040113.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040113.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040113/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040113 none O=C([O-])CCOC1=CC=CC(CN=NC2=NC=CC=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.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: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 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]
0  hydrogens need rotated
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, 51, 51, 51, 51, 51, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 201, 201, 201, 201, 51, 51, 51, 9, 9, 1, 1, 1, 51] 201
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, 34])
total number of confs: 272
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040113 none O=C([O-])CCOC1=CC=CC(CN=NC2=NC=CC=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.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: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 10, 17, 10, 6, 1, 1, 1, 1, 1, 1, 1, 9, 51, 51, 51, 51, 51, 51, 51, 51, 1, 10, 10, 10, 10, 1, 1, 1, 9, 9, 51, 51, 51, 1] 201
rigid atoms, others: [34, 5, 6, 7, 8, 9, 10, 11, 21, 26, 27, 28] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31, 32, 33])
total number of confs: 132
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040113 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040113
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040113/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040113
Building REAL300000040114
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040114'
/scratch/stefan/7769621/working/building/REAL300000040114 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040114

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040114/0 /scratch/stefan/7769621/working/building/REAL300000040114 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 162)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/162
`/scratch/stefan/7769621/working/3D/162' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC=C1COC1=CC=CC(CN=NC2=NC=CC=C2Cl)=C1)

`REAL300000040114.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040114.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040114/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040114 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(CN=NC2=NC=CC=C2Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'N.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', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 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, 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, 201, 201, 201, 201, 201, 201, 201, 141, 141, 79, 79, 79, 79, 79, 18, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 79, 201, 201, 201, 201, 141, 141, 79, 79, 79, 18, 18, 1, 1, 1, 79] 201
rigid atoms, others: [38, 39, 40, 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, 41])
total number of confs: 359
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: REAL300000040114 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(CN=NC2=NC=CC=C2Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'N.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', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 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, 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, 7, 9, 7, 7, 6, 7, 7, 2, 2, 1, 1, 1, 1, 1, 1, 1, 9, 63, 63, 79, 79, 79, 79, 79, 79, 1, 7, 6, 7, 7, 2, 2, 1, 1, 1, 9, 9, 79, 79, 79, 1] 201
rigid atoms, others: [33, 34, 35, 41, 10, 11, 12, 13, 14, 15, 16, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40])
total number of confs: 142
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040114 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(CN=NC2=NC=CC=C2Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'N.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', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 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, 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, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 42, 181, 181, 201, 201, 201, 201, 201, 201, 7, 1, 1, 1, 1, 4, 4, 7, 7, 7, 42, 42, 201, 201, 201, 7] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29, 30] set([0, 2, 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])
total number of confs: 360
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040114 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040114
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040114/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040114
Building REAL300000040115
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040115'
/scratch/stefan/7769621/working/building/REAL300000040115 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040115

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040115/0 /scratch/stefan/7769621/working/building/REAL300000040115 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 163)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/163
`/scratch/stefan/7769621/working/3D/163' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC2=NC=CC=C2Cl)C=C1[N+](=O)[O-])

`REAL300000040115.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040115.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040115/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040115 none O=C([O-])COC1=CC=C(C=NNC2=NC=CC=C2Cl)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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 8, 1, 1, 1, 1, 16, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [35, 35, 35, 35, 21, 21, 29, 29, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 35, 35, 29, 29, 14, 4, 1, 1, 1, 29] 35
rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 92
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040115 none O=C([O-])COC1=CC=C(C=NNC2=NC=CC=C2Cl)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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 8, 1, 1, 1, 1, 16, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 7, 7, 23, 29, 29, 29, 29, 29, 29, 1, 1, 1, 2, 2, 5, 5, 1, 1, 7, 23, 29, 29, 29, 1] 35
rigid atoms, others: [33, 4, 5, 6, 7, 8, 9, 19, 20, 21, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 28, 29, 30, 31, 32])
total number of confs: 87
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040115 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040115
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040115/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040115
Building REAL300000040116
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040116'
/scratch/stefan/7769621/working/building/REAL300000040116 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040116

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040116/0 /scratch/stefan/7769621/working/building/REAL300000040116 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 164)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/164
`/scratch/stefan/7769621/working/3D/164' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])OC(COC2=CC=C(CN=NC3=NC=CC=C3Cl)C=C2)=C1)

`REAL300000040116.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040116.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040116/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040116 none CC1=C(C(=O)[O-])OC(COC2=CC=C(CN=NC3=NC=CC=C3Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 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, 60, 60, 43, 14, 60, 60, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 60, 60, 201, 201, 201, 201, 60, 60, 60, 60, 13, 13, 1, 1, 1, 60, 60, 201] 201
rigid atoms, others: [36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41])
total number of confs: 430
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: REAL300000040116 none CC1=C(C(=O)[O-])OC(COC2=CC=C(CN=NC3=NC=CC=C3Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 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, 6, 6, 6, 11, 11, 6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 53, 53, 59, 59, 59, 59, 59, 60, 1, 1, 6, 6, 6, 6, 1, 1, 1, 1, 8, 8, 59, 59, 60, 1, 1, 6] 201
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 40, 39, 24, 25, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41])
total number of confs: 120
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040116 none CC1=C(C(=O)[O-])OC(COC2=CC=C(CN=NC3=NC=CC=C3Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 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, 2, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 35, 191, 191, 201, 201, 201, 201, 201, 201, 6, 6, 1, 2, 2, 2, 6, 6, 6, 6, 35, 35, 201, 201, 201, 5, 6, 1] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 41, 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])
total number of confs: 342
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040116 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040116
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040116/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040116
Building REAL300000040117
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040117'
/scratch/stefan/7769621/working/building/REAL300000040117 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040117

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040117/0 /scratch/stefan/7769621/working/building/REAL300000040117 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 165)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/165
`/scratch/stefan/7769621/working/3D/165' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(COC2=CC=CC(CN=NC3=NC=CC=C3Cl)=C2)=C1)

`REAL300000040117.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040117.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040117/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040117 none O=C([O-])C1=CC=CC(COC2=CC=CC(CN=NC3=NC=CC=C3Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'N.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: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 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, 7, 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, 201, 201, 201, 201, 201, 61, 61, 36, 36, 36, 36, 36, 11, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 36, 201, 201, 201, 201, 61, 61, 36, 36, 36, 11, 11, 1, 1, 1, 36, 201] 201
rigid atoms, others: [37, 38, 39, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41])
total number of confs: 310
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: REAL300000040117 none O=C([O-])C1=CC=CC(COC2=CC=CC(CN=NC3=NC=CC=C3Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'N.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: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 11, 10, 11, 11, 2, 2, 1, 1, 1, 1, 1, 1, 1, 9, 36, 36, 36, 36, 36, 36, 36, 36, 1, 11, 10, 11, 11, 2, 2, 1, 1, 1, 9, 9, 36, 36, 36, 1, 11] 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: 79
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040117 none O=C([O-])C1=CC=CC(COC2=CC=CC(CN=NC3=NC=CC=C3Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'N.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: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 11, 66, 201, 201, 201, 201, 201, 201, 201, 201, 11, 1, 1, 1, 1, 6, 6, 11, 11, 11, 66, 66, 201, 201, 201, 11, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 26, 27, 28, 29] set([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: 419
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040117 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040117
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040117/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040117
Building REAL300000040118
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040118'
/scratch/stefan/7769621/working/building/REAL300000040118 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040118

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040118/0 /scratch/stefan/7769621/working/building/REAL300000040118 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 166)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/166
`/scratch/stefan/7769621/working/3D/166' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=CC(CN=NC2=NC=CC=C2Cl)=C1)

`REAL300000040118.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040118.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040118/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040118 none O=C([O-])COC1=CC=CC(CN=NC2=NC=CC=C2Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 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]
0  hydrogens need rotated
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, 170, 55, 55, 55, 55, 55, 11, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 55, 201, 201, 55, 55, 55, 11, 11, 1, 1, 1, 55] 201
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 434
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040118 none O=C([O-])COC1=CC=CC(CN=NC2=NC=CC=C2Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 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]
0  hydrogens 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, 16, 29, 6, 1, 1, 1, 1, 1, 1, 1, 9, 53, 53, 55, 55, 55, 55, 55, 55, 1, 16, 16, 1, 1, 1, 9, 9, 55, 55, 55, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 20, 23, 24, 25, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 26, 27, 28, 29, 30])
total number of confs: 177
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040118 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040118
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040118/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040118
Building REAL300000040119
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040119'
/scratch/stefan/7769621/working/building/REAL300000040119 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040119

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040119/0 /scratch/stefan/7769621/working/building/REAL300000040119 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 167)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/167
`/scratch/stefan/7769621/working/3D/167' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(COC2=CC=C(CN=NC3=NC=CC=C3Cl)C=C2)OC=C1)

`REAL300000040119.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040119.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040119/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040119 none O=C([O-])C1=C(COC2=CC=C(CN=NC3=NC=CC=C3Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 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, 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]
0  hydrogens need rotated
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, 121, 101, 76, 31, 101, 101, 30, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 101, 101, 201, 201, 201, 121, 121, 101, 101, 30, 30, 1, 1, 1, 101, 101, 201, 201] 201
rigid atoms, others: [32, 33, 34, 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, 35, 36, 37, 38])
total number of confs: 646
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: REAL300000040119 none O=C([O-])C1=C(COC2=CC=C(CN=NC3=NC=CC=C3Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 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, 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]
0  hydrogens 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, 8, 66, 66, 100, 100, 100, 100, 100, 101, 1, 1, 9, 9, 9, 5, 5, 1, 1, 8, 8, 100, 100, 101, 1, 1, 9, 9] 201
rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 189
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040119 none O=C([O-])C1=C(COC2=CC=C(CN=NC3=NC=CC=C3Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 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, 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]
0  hydrogens 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, 48, 194, 195, 201, 201, 201, 201, 201, 201, 9, 9, 1, 1, 1, 5, 5, 9, 9, 48, 48, 201, 201, 201, 9, 9, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 38, 23, 24, 25, 37] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 371
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040119 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040119
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040119/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040119
Building REAL300000040120
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040120'
/scratch/stefan/7769621/working/building/REAL300000040120 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040120

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040120/0 /scratch/stefan/7769621/working/building/REAL300000040120 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 168)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/168
`/scratch/stefan/7769621/working/3D/168' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CN=NC2=NC=CC=C2Cl)C(OCC(=O)[O-])=C1)

`REAL300000040120.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040120.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040120/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040120 none COC1=CC=C(CN=NC2=NC=CC=C2Cl)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 12, 5, 1, 11, 11, 1, 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]
0  hydrogens 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, 46, 20, 46, 46, 16, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 129, 195, 201, 201, 46, 62, 62, 62, 46, 46, 15, 15, 1, 1, 1, 195, 195, 46] 201
rigid atoms, others: [32, 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, 33, 34, 35])
total number of confs: 669
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040120 none COC1=CC=C(CN=NC2=NC=CC=C2Cl)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 12, 5, 1, 11, 11, 1, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 6, 40, 40, 46, 46, 46, 46, 46, 46, 1, 1, 7, 29, 51, 51, 1, 3, 3, 3, 1, 1, 6, 6, 46, 46, 46, 29, 29, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 16, 17, 35, 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])
total number of confs: 243
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040120 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040120
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040120/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040120
Building REAL300000040121
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040121'
/scratch/stefan/7769621/working/building/REAL300000040121 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040121

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040121/0 /scratch/stefan/7769621/working/building/REAL300000040121 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 169)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/169
`/scratch/stefan/7769621/working/3D/169' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C(F)(F)OC1=CC=C(CN=NC2=NC=CC=C2Cl)C=C1)

`REAL300000040121.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040121.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040121/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040121 none O=C([O-])C(F)(F)OC1=CC=C(CN=NC2=NC=CC=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 139, 201, 201, 38, 10, 48, 48, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 9, 9, 1, 1, 1, 48, 48] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 628
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040121 none O=C([O-])C(F)(F)OC1=CC=C(CN=NC2=NC=CC=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 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, 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: [24, 18, 24, 7, 18, 18, 1, 1, 1, 1, 1, 1, 7, 47, 47, 47, 47, 47, 47, 47, 48, 1, 1, 1, 1, 7, 7, 47, 47, 48, 1, 1] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 145
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040121 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040121
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040121/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040121
Building REAL300000040122
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040122'
/scratch/stefan/7769621/working/building/REAL300000040122 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040122

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040122/0 /scratch/stefan/7769621/working/building/REAL300000040122 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 170)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/170
`/scratch/stefan/7769621/working/3D/170' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(C(=O)[O-])=CC(Br)=C1CN=NC1=NC=CC=C1Cl)

`REAL300000040122.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040122.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040122/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040122 none CN1C(C(=O)[O-])=CC(Br)=C1CN=NC1=NC=CC=C1Cl 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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [54, 54, 54, 54, 54, 54, 54, 54, 54, 30, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 29, 29, 1, 1, 1] 54
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25])
total number of confs: 133
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040122 none CN1C(C(=O)[O-])=CC(Br)=C1CN=NC1=NC=CC=C1Cl 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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 41, 41, 54, 54, 54, 54, 54, 54, 2, 2, 2, 1, 7, 7, 54, 54, 54] 54
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28])
total number of confs: 93
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040122 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040122/1 /scratch/stefan/7769621/working/building/REAL300000040122 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 171)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/171
`/scratch/stefan/7769621/working/3D/171' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=NC=CC=C1Cl)

`REAL300000040122.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040122.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040122/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040122 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=NC=CC=C1Cl 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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [56, 56, 56, 56, 56, 56, 56, 56, 56, 33, 33, 11, 1, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 33, 11, 1, 1, 1] 56
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25])
total number of confs: 92
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040122 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=NC=CC=C1Cl 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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 13, 13, 41, 56, 56, 56, 56, 56, 56, 2, 2, 2, 1, 13, 41, 56, 56, 56] 56
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])
total number of confs: 140
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040122 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040122
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040122/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040122/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040122
Building REAL300000040123
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040123'
/scratch/stefan/7769621/working/building/REAL300000040123 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040123

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040123/0 /scratch/stefan/7769621/working/building/REAL300000040123 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 172)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/172
`/scratch/stefan/7769621/working/3D/172' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(CN=NC2=NC=CC=C2Cl)C=C1Br)

`REAL300000040123.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040123.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040123/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040123 none O=C([O-])COC1=CC=C(CN=NC2=NC=CC=C2Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 17, 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, 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, 165, 57, 22, 58, 58, 11, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 201, 201, 58, 58, 11, 11, 1, 1, 1, 58] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 591
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040123 none O=C([O-])COC1=CC=C(CN=NC2=NC=CC=C2Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 17, 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, 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: [24, 20, 24, 7, 1, 1, 1, 1, 1, 1, 9, 56, 56, 58, 58, 58, 58, 58, 58, 1, 1, 1, 20, 20, 1, 1, 9, 9, 58, 58, 58, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 19, 20, 21, 24, 25, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27, 28, 29, 30])
total number of confs: 167
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040123 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040123/1 /scratch/stefan/7769621/working/building/REAL300000040123 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 173)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/173
`/scratch/stefan/7769621/working/3D/173' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC2=NC=CC=C2Cl)C=C1Br)

`REAL300000040123.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040123.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040123/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040123 none O=C([O-])COC1=CC=C(C=NNC2=NC=CC=C2Cl)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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', '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, 8, 1, 1, 1, 1, 16, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 159, 72, 45, 75, 74, 27, 27, 5, 1, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 201, 201, 75, 74, 27, 5, 1, 1, 1, 75] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 583
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040123 none O=C([O-])COC1=CC=C(C=NNC2=NC=CC=C2Cl)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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', '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, 8, 1, 1, 1, 1, 16, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [57, 37, 57, 7, 1, 1, 1, 1, 1, 1, 6, 6, 38, 74, 74, 74, 74, 74, 74, 1, 1, 1, 37, 37, 1, 1, 6, 38, 74, 74, 75, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 19, 20, 21, 24, 25, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27, 28, 29, 30])
total number of confs: 333
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040123 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040123
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040123/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040123/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040123
Building REAL300000040124
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040124'
/scratch/stefan/7769621/working/building/REAL300000040124 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040124

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040124/0 /scratch/stefan/7769621/working/building/REAL300000040124 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 174)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/174
`/scratch/stefan/7769621/working/3D/174' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=NC=CC=C2Cl)C=C1)

`REAL300000040124.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040124.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040124/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040124 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=NC=CC=C2Cl)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.ar', 'N.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']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 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, 3, 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, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 40, 40, 11, 1, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 56, 56, 40, 11, 1, 1, 1, 56, 56] 56
rigid atoms, others: [32, 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, 33, 34])
total number of confs: 92
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040124 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=NC=CC=C2Cl)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.ar', 'N.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']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 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, 3, 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: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 6, 6, 27, 56, 56, 56, 56, 56, 56, 1, 1, 4, 4, 4, 1, 6, 27, 56, 56, 56, 1, 1] 56
rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 9, 10, 11, 12, 34, 22, 23, 27] set([0, 32, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29, 30, 31])
total number of confs: 118
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040124 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040124/1 /scratch/stefan/7769621/working/building/REAL300000040124 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 175)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/175
`/scratch/stefan/7769621/working/3D/175' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(CN=NC2=NC=CC=C2Cl)C=C1)

`REAL300000040124.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040124.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040124/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040124 none COC1=C2OC(C(=O)[O-])=CC2=C(CN=NC2=NC=CC=C2Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.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']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 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, 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
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, 120, 120, 48, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 120, 120, 120, 120, 120, 120, 47, 47, 1, 1, 1, 120, 120] 120
rigid atoms, others: [32, 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, 33, 34])
total number of confs: 249
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040124 none COC1=C2OC(C(=O)[O-])=CC2=C(CN=NC2=NC=CC=C2Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.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']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 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, 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
120  conformations in input
total number of sets (complete confs): 120
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, 61, 61, 120, 120, 120, 120, 120, 120, 1, 1, 4, 4, 4, 1, 8, 8, 120, 120, 120, 1, 1] 120
rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 9, 10, 11, 12, 34, 22, 23, 27] set([0, 32, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29, 30, 31])
total number of confs: 197
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040124 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040124
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040124/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040124/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040124
Building REAL300000040125
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040125'
/scratch/stefan/7769621/working/building/REAL300000040125 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040125

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040125/0 /scratch/stefan/7769621/working/building/REAL300000040125 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 176)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/176
`/scratch/stefan/7769621/working/3D/176' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(N=NC1=NC=CC=C1Cl)C1=CC=C(C(=O)[O-])C=C1)

`REAL300000040125.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040125.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040125/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040125 none CCC(N=NC1=NC=CC=C1Cl)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [12, 7, 1, 7, 28, 28, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 2, 2, 1, 1, 13, 13, 13, 13, 13, 7, 36, 36, 36, 1, 1, 1, 1] 42
rigid atoms, others: [32, 33, 2, 12, 13, 14, 15, 16, 19, 20, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 106
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040125 none CCC(N=NC1=NC=CC=C1Cl)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [28, 26, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 26, 36, 36, 26, 36, 36, 36, 36, 36, 34, 34, 34, 34, 34, 26, 1, 1, 1, 36, 36, 36, 36] 42
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 213
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040125 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040125
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040125/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040125
Building REAL300000040126
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040126'
/scratch/stefan/7769621/working/building/REAL300000040126 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040126

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040126/0 /scratch/stefan/7769621/working/building/REAL300000040126 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 177)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/177
`/scratch/stefan/7769621/working/3D/177' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NC=CC=C1Cl)C1=CC(C(=O)[O-])=CC=C1O)

`REAL300000040126.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040126.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040126/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040126 none CC(=NNC1=NC=CC=C1Cl)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 3, 7, 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]
1  hydrogens need rotated
158  conformations in input
total number of sets (complete confs): 158
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 37, 79, 79, 79, 79, 79, 79, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 9, 9, 37, 79, 79, 79, 1, 1, 1, 2] 158
rigid atoms, others: [1, 11, 12, 13, 14, 17, 18, 19, 20, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 161
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040126 none CC(=NNC1=NC=CC=C1Cl)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 3, 7, 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]
1  hydrogens need rotated
158  conformations in input
total number of sets (complete confs): 158
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 9, 1, 1, 1, 1, 1, 1, 1, 1, 30, 79, 79, 79, 79, 79, 79, 79, 79, 79, 30, 30, 30, 9, 1, 1, 1, 79, 79, 79, 158] 158
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31])
total number of confs: 286
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040126 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040126/1 /scratch/stefan/7769621/working/building/REAL300000040126 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 178)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/178
`/scratch/stefan/7769621/working/3D/178' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=NC=CC=C1Cl)C1=CC(C(=O)[O-])=CC=C1O)

`REAL300000040126.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040126.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040126/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040126 none CC(N=NC1=NC=CC=C1Cl)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 39, 39, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 9, 9, 9, 45, 45, 45, 1, 1, 1, 2] 90
rigid atoms, others: [1, 11, 12, 13, 14, 17, 18, 19, 20, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 81
number of broken/clashed sets: 34
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040126 none CC(N=NC1=NC=CC=C1Cl)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [28, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 28, 45, 45, 45, 45, 45, 45, 45, 45, 45, 28, 28, 28, 28, 1, 1, 1, 45, 45, 45, 90] 90
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31])
total number of confs: 206
number of broken/clashed sets: 34
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040126 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040126
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040126/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040126/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040126
Building REAL300000040127
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040127'
/scratch/stefan/7769621/working/building/REAL300000040127 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040127

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040127/0 /scratch/stefan/7769621/working/building/REAL300000040127 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 179)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/179
`/scratch/stefan/7769621/working/3D/179' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(N=NC1=NC=CC=C1Cl)C1=CC(C(=O)[O-])=CC=C1F)

`REAL300000040127.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040127.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040127/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040127 none CCC(N=NC1=NC=CC=C1Cl)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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
86  conformations in input
total number of sets (complete confs): 86
using faster count positions algorithm for large data
unique positions, atoms: [17, 11, 1, 11, 54, 54, 68, 68, 68, 68, 68, 68, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 21, 21, 21, 21, 21, 11, 68, 68, 68, 1, 1, 1] 86
rigid atoms, others: [32, 33, 2, 12, 13, 14, 15, 18, 19, 20, 21, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 191
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040127 none CCC(N=NC1=NC=CC=C1Cl)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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
86  conformations in input
total number of sets (complete confs): 86
using faster count positions algorithm for large data
unique positions, atoms: [39, 29, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 29, 68, 68, 68, 68, 68, 68, 68, 68, 68, 45, 45, 45, 45, 45, 29, 1, 1, 1, 68, 68, 68] 86
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33])
total number of confs: 265
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040127 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040127/1 /scratch/stefan/7769621/working/building/REAL300000040127 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 180)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/180
`/scratch/stefan/7769621/working/3D/180' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC1=NC=CC=C1Cl)C1=CC(C(=O)[O-])=CC=C1F)

`REAL300000040127.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040127.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040127/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040127 none CCC(=NNC1=NC=CC=C1Cl)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 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
166  conformations in input
total number of sets (complete confs): 166
using faster count positions algorithm for large data
unique positions, atoms: [36, 12, 1, 12, 12, 77, 147, 147, 147, 147, 147, 147, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 37, 37, 37, 36, 36, 77, 147, 147, 147, 1, 1, 1] 166
rigid atoms, others: [32, 33, 2, 12, 13, 14, 15, 18, 19, 20, 21, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 404
number of broken/clashed sets: 59
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040127 none CCC(=NNC1=NC=CC=C1Cl)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 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
166  conformations in input
total number of sets (complete confs): 166
using faster count positions algorithm for large data
unique positions, atoms: [94, 49, 49, 11, 1, 1, 1, 1, 1, 1, 1, 1, 49, 147, 147, 147, 147, 147, 147, 147, 147, 147, 95, 95, 95, 94, 94, 11, 1, 1, 1, 147, 147, 147] 166
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33])
total number of confs: 440
number of broken/clashed sets: 59
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040127 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040127
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040127/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040127/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040127
Building REAL300000040128
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040128'
/scratch/stefan/7769621/working/building/REAL300000040128 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040128

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040128/0 /scratch/stefan/7769621/working/building/REAL300000040128 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 181)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/181
`/scratch/stefan/7769621/working/3D/181' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=NNC(CN=NC3=NC=CC=C3Cl)=C2C=C1)

`REAL300000040128.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040128.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040128/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040128 none O=C([O-])C1=CC2=NNC(CN=NC3=NC=CC=C3Cl)=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [53, 53, 53, 53, 53, 53, 53, 53, 25, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 25, 25, 1, 1, 1, 53, 53] 53
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 29, 30])
total number of confs: 122
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040128 none O=C([O-])C1=CC2=NNC(CN=NC3=NC=CC=C3Cl)=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 9, 50, 51, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 9, 9, 53, 53, 53, 1, 1] 53
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28])
total number of confs: 88
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040128 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040128/1 /scratch/stefan/7769621/working/building/REAL300000040128 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 182)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/182
`/scratch/stefan/7769621/working/3D/182' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=NNC(C=NNC3=NC=CC=C3Cl)=C2C=C1)

`REAL300000040128.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040128.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040128/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040128 none O=C([O-])C1=CC2=NNC(C=NNC3=NC=CC=C3Cl)=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 26, 26, 10, 1, 1, 1, 1, 1, 1, 1, 1, 29, 31, 31, 31, 31, 26, 10, 1, 1, 1, 31, 31] 31
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 29, 30])
total number of confs: 57
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040128 none O=C([O-])C1=CC2=NNC(C=NNC3=NC=CC=C3Cl)=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 6, 16, 31, 31, 31, 1, 1] 31
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 29, 30] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28])
total number of confs: 61
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040128 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040128
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040128/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040128/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040128
Building REAL300000040129
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040129'
/scratch/stefan/7769621/working/building/REAL300000040129 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040129

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040129/0 /scratch/stefan/7769621/working/building/REAL300000040129 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 183)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/183
`/scratch/stefan/7769621/working/3D/183' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=NC=CC=C1Cl)C1=CC=C(C(=O)[O-])C(F)=C1)

`REAL300000040129.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040129.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040129/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040129 none CC(N=NC1=NC=CC=C1Cl)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 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, 7, 2, 2, 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: [13, 1, 13, 65, 65, 103, 103, 103, 103, 103, 103, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 13, 13, 13, 13, 103, 103, 103, 1, 1, 1] 103
rigid atoms, others: [1, 11, 12, 13, 14, 15, 18, 19, 20, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 177
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040129 none CC(N=NC1=NC=CC=C1Cl)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 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, 7, 2, 2, 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: [36, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 36, 103, 103, 103, 103, 103, 103, 103, 103, 103, 36, 36, 36, 36, 1, 1, 1, 103, 103, 103] 103
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30])
total number of confs: 211
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040129 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040129/1 /scratch/stefan/7769621/working/building/REAL300000040129 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 184)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/184
`/scratch/stefan/7769621/working/3D/184' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NC=CC=C1Cl)C1=CC=C(C(=O)[O-])C(F)=C1)

`REAL300000040129.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040129.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040129/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040129 none CC(=NNC1=NC=CC=C1Cl)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 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]
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: [11, 1, 11, 11, 61, 136, 136, 136, 136, 136, 136, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 11, 11, 11, 61, 136, 136, 136, 1, 1, 1] 136
rigid atoms, others: [1, 11, 12, 13, 14, 15, 18, 19, 20, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 263
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040129 none CC(=NNC1=NC=CC=C1Cl)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 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]
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: [48, 48, 11, 1, 1, 1, 1, 1, 1, 1, 1, 49, 136, 136, 136, 136, 136, 136, 136, 136, 136, 49, 49, 49, 11, 1, 1, 1, 136, 136, 136] 136
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30])
total number of confs: 210
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040129 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040129
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040129/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040129/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040129
Building REAL300000040130
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040130'
/scratch/stefan/7769621/working/building/REAL300000040130 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040130

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040130/0 /scratch/stefan/7769621/working/building/REAL300000040130 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 185)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/185
`/scratch/stefan/7769621/working/3D/185' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=NC=CC=C2Cl)=C([N+](=O)[O-])C=C1OCC(=O)[O-])

`REAL300000040130.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040130.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040130/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040130 none COC1=CC(C=NNC2=NC=CC=C2Cl)=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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 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, 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]
0  hydrogens 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, 69, 69, 69, 34, 33, 5, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 68, 69, 179, 201, 201, 201, 111, 111, 111, 69, 33, 5, 1, 1, 1, 69, 201, 201] 201
rigid atoms, others: [32, 33, 34, 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, 35, 36, 37])
total number of confs: 466
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040130 none COC1=CC(C=NNC2=NC=CC=C2Cl)=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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 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, 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]
0  hydrogens 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, 33, 69, 69, 69, 69, 69, 69, 1, 1, 2, 2, 1, 1, 1, 9, 17, 23, 23, 4, 4, 4, 1, 7, 33, 69, 69, 69, 1, 17, 17] 201
rigid atoms, others: [1, 2, 3, 4, 5, 35, 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, 36, 37])
total number of confs: 217
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040130 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040130
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040130/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040130
Building REAL300000040131
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040131'
/scratch/stefan/7769621/working/building/REAL300000040131 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040131

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040131/0 /scratch/stefan/7769621/working/building/REAL300000040131 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 186)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/186
`/scratch/stefan/7769621/working/3D/186' -> `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=C1CN=NC1=NC=CC=C1Cl)

`REAL300000040131.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040131.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040131/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040131 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1CN=NC1=NC=CC=C1Cl 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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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, 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
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [128, 96, 128, 188, 188, 188, 96, 96, 96, 96, 96, 96, 96, 96, 96, 40, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 128, 128, 128, 188, 188, 96, 96, 96, 40, 40, 1, 1, 1] 188
rigid atoms, others: [36, 37, 38, 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])
total number of confs: 635
number of broken/clashed sets: 40
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040131 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1CN=NC1=NC=CC=C1Cl 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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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, 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
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 18, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 45, 46, 96, 96, 96, 96, 96, 96, 4, 4, 4, 18, 18, 1, 1, 1, 7, 7, 96, 96, 96] 188
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])
total number of confs: 255
number of broken/clashed sets: 40
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040131 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040131/1 /scratch/stefan/7769621/working/building/REAL300000040131 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 187)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/187
`/scratch/stefan/7769621/working/3D/187' -> `1.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=NNC1=NC=CC=C1Cl)

`REAL300000040131.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040131.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040131/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040131 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNC1=NC=CC=C1Cl 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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [57, 51, 57, 64, 64, 64, 51, 51, 35, 51, 51, 51, 51, 51, 51, 35, 35, 10, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 64, 64, 51, 51, 51, 35, 10, 1, 1, 1] 64
rigid atoms, others: [36, 37, 38, 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])
total number of confs: 220
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040131 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNC1=NC=CC=C1Cl 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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 16, 25, 25, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 4, 4, 24, 51, 51, 51, 51, 51, 51, 4, 4, 4, 16, 16, 1, 1, 1, 4, 24, 51, 51, 51] 64
rigid atoms, others: [32, 1, 33, 6, 7, 8, 9, 10, 14, 15, 16, 31] set([0, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38])
total number of confs: 181
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040131 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040131
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040131/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040131/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040131
Building REAL300000040132
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040132'
/scratch/stefan/7769621/working/building/REAL300000040132 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040132

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040132/0 /scratch/stefan/7769621/working/building/REAL300000040132 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 188)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/188
`/scratch/stefan/7769621/working/3D/188' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=NC=CC=C1Cl)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1)

`REAL300000040132.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040132.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040132/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040132 none CC(N=NC1=NC=CC=C1Cl)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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]
dock color type numbers: [7, 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]
0  hydrogens 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, 19, 66, 199, 199, 201, 201, 201, 201, 201, 201, 8, 19, 19, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 19, 19, 66, 66, 66, 66, 201, 201, 201, 19, 19, 1, 1, 1, 1, 19, 19] 201
rigid atoms, others: [36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41])
total number of confs: 442
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: REAL300000040132 none CC(N=NC1=NC=CC=C1Cl)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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]
dock color type numbers: [7, 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]
0  hydrogens 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, 41, 41, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 9, 19, 19, 9, 11, 19, 19, 19, 19, 1, 1, 7, 7, 7, 7, 63, 63, 63, 1, 1, 19, 19, 19, 19, 1, 1] 201
rigid atoms, others: [1, 34, 35, 40, 41, 11, 12, 13, 14, 15, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39])
total number of confs: 176
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040132 none CC(N=NC1=NC=CC=C1Cl)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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]
dock color type numbers: [7, 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]
0  hydrogens 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, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 28, 63, 63, 28, 30, 187, 201, 201, 187, 187, 201, 201, 201, 201, 63, 63, 28, 28, 28, 28, 1, 1, 1, 63, 63, 201, 201, 201, 201, 63, 63] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 506
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040132 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040132/1 /scratch/stefan/7769621/working/building/REAL300000040132 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 189)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/189
`/scratch/stefan/7769621/working/3D/189' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NC=CC=C1Cl)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1)

`REAL300000040132.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040132.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040132/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040132 none CC(=NNC1=NC=CC=C1Cl)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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 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]
0  hydrogens 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, 8, 59, 59, 177, 201, 201, 201, 201, 201, 201, 8, 19, 19, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 19, 19, 59, 59, 59, 177, 201, 201, 201, 19, 19, 1, 1, 1, 1, 19, 19] 201
rigid atoms, others: [36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41])
total number of confs: 525
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: REAL300000040132 none CC(=NNC1=NC=CC=C1Cl)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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 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]
0  hydrogens 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, 30, 73, 73, 73, 73, 73, 73, 1, 1, 1, 1, 1, 9, 19, 19, 15, 19, 19, 19, 19, 19, 1, 1, 6, 6, 6, 30, 73, 73, 73, 1, 1, 19, 19, 19, 19, 1, 1] 201
rigid atoms, others: [1, 34, 35, 40, 41, 11, 12, 13, 14, 15, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39])
total number of confs: 180
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040132 none CC(=NNC1=NC=CC=C1Cl)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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 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]
0  hydrogens 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, 7, 1, 1, 1, 1, 1, 1, 1, 1, 27, 73, 73, 45, 38, 174, 201, 201, 201, 201, 201, 201, 201, 201, 73, 73, 28, 28, 28, 7, 1, 1, 1, 73, 73, 201, 201, 201, 201, 73, 73] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 409
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040132 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040132
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040132/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040132/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040132
Building REAL300000040133
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040133'
/scratch/stefan/7769621/working/building/REAL300000040133 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040133

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040133/0 /scratch/stefan/7769621/working/building/REAL300000040133 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 190)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/190
`/scratch/stefan/7769621/working/3D/190' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(CN=NC2=NC=CC=C2Cl)=CC=C1OCCC(=O)[O-])

`REAL300000040133.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040133.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040133/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040133 none COC1=CC(CN=NC2=NC=CC=C2Cl)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 1, 11, 11, 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, 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]
0  hydrogens 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, 47, 47, 47, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 147, 189, 189, 201, 190, 87, 87, 87, 47, 9, 9, 1, 1, 1, 47, 47, 189, 189, 189, 189] 201
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, 37, 38])
total number of confs: 579
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040133 none COC1=CC(CN=NC2=NC=CC=C2Cl)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 1, 11, 11, 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, 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]
0  hydrogens 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, 46, 46, 46, 46, 46, 46, 46, 47, 1, 1, 1, 1, 5, 11, 11, 19, 17, 3, 3, 3, 1, 6, 6, 46, 46, 47, 1, 1, 11, 11, 11, 11] 201
rigid atoms, others: [1, 2, 3, 4, 5, 33, 34, 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, 35, 36, 37, 38])
total number of confs: 135
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040133 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040133/1 /scratch/stefan/7769621/working/building/REAL300000040133 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 191)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/191
`/scratch/stefan/7769621/working/3D/191' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=NC=CC=C2Cl)=CC=C1OCCC(=O)[O-])

`REAL300000040133.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040133.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040133/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040133 none COC1=CC(C=NNC2=NC=CC=C2Cl)=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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 1, 11, 11, 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, 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]
0  hydrogens 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, 48, 48, 48, 18, 17, 3, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 137, 185, 185, 201, 191, 79, 79, 79, 48, 17, 3, 1, 1, 1, 48, 48, 185, 185, 185, 185] 201
rigid atoms, others: [32, 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, 33, 34, 35, 36, 37, 38])
total number of confs: 553
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040133 none COC1=CC(C=NNC2=NC=CC=C2Cl)=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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 1, 11, 11, 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, 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]
0  hydrogens 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, 27, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 9, 30, 32, 47, 45, 3, 3, 3, 1, 7, 27, 48, 48, 48, 1, 1, 30, 30, 32, 32] 201
rigid atoms, others: [1, 2, 3, 4, 5, 33, 34, 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, 35, 36, 37, 38])
total number of confs: 264
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040133 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040133
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040133/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040133/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040133
Building REAL300000040134
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040134'
/scratch/stefan/7769621/working/building/REAL300000040134 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040134

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040134/0 /scratch/stefan/7769621/working/building/REAL300000040134 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 192)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/192
`/scratch/stefan/7769621/working/3D/192' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC2=NC=CC=C2Cl)C(Cl)=C1)

`REAL300000040134.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040134.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040134/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040134 none O=C([O-])C1=CC=C(C=NNC2=NC=CC=C2Cl)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [42, 42, 42, 34, 42, 42, 33, 33, 11, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 33, 11, 1, 1, 1, 42] 42
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 27])
total number of confs: 102
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040134 none O=C([O-])C1=CC=C(C=NNC2=NC=CC=C2Cl)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 30, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 1, 10, 30, 42, 42, 42, 1] 42
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26])
total number of confs: 100
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040134 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040134/1 /scratch/stefan/7769621/working/building/REAL300000040134 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 193)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/193
`/scratch/stefan/7769621/working/3D/193' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(CN=NC2=NC=CC=C2Cl)C(Cl)=C1)

`REAL300000040134.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040134.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040134/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040134 none O=C([O-])C1=CC=C(CN=NC2=NC=CC=C2Cl)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 16, 1, 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]
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, 59, 24, 59, 59, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 23, 23, 1, 1, 1, 59] 59
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 27])
total number of confs: 251
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040134 none O=C([O-])C1=CC=C(CN=NC2=NC=CC=C2Cl)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 16, 1, 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]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 44, 44, 59, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 8, 8, 59, 59, 59, 1] 59
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 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/7769621/working/building/REAL300000040134 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040134
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040134/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040134/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040134
Building REAL300000040135
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040135'
/scratch/stefan/7769621/working/building/REAL300000040135 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040135

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040135/0 /scratch/stefan/7769621/working/building/REAL300000040135 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 194)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/194
`/scratch/stefan/7769621/working/3D/194' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NC=CC=C1Cl)C1=CC(C(=O)[O-])=C(C)N=C1C)

`REAL300000040135.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040135.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040135/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040135 none CC(=NNC1=NC=CC=C1Cl)C1=CC(C(=O)[O-])=C(C)N=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 10, 10, 48, 106, 106, 106, 106, 106, 106, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 10, 10, 10, 48, 106, 106, 106, 1, 2, 2, 2, 2, 2, 2] 106
rigid atoms, others: [1, 11, 12, 13, 14, 17, 18, 19, 20, 21, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35])
total number of confs: 217
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040135 none CC(=NNC1=NC=CC=C1Cl)C1=CC(C(=O)[O-])=C(C)N=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [43, 44, 12, 1, 1, 1, 1, 1, 1, 1, 1, 44, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 44, 44, 44, 12, 1, 1, 1, 106, 106, 106, 106, 106, 106, 106] 106
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 164
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040135 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040135/1 /scratch/stefan/7769621/working/building/REAL300000040135 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 195)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/195
`/scratch/stefan/7769621/working/3D/195' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C)=C(C(=O)[O-])C=C1C(C)N=NC1=NC=CC=C1Cl)

`REAL300000040135.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040135.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040135/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040135 none CC1=NC(C)=C(C(=O)[O-])C=C1C(C)N=NC1=NC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 11, 1, 1, 5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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, 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]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 24, 7, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 24, 24, 24, 24, 1, 1, 1] 31
rigid atoms, others: [33, 34, 35, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 88
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040135 none CC1=NC(C)=C(C(=O)[O-])C=C1C(C)N=NC1=NC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 11, 1, 1, 5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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, 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]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 26, 26, 31, 31, 31, 31, 31, 31, 2, 2, 2, 2, 2, 2, 1, 5, 5, 5, 5, 31, 31, 31] 31
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 28] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 65
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040135 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040135
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040135/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040135/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040135
Building REAL300000040136
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040136'
/scratch/stefan/7769621/working/building/REAL300000040136 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040136

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040136/0 /scratch/stefan/7769621/working/building/REAL300000040136 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 196)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/196
`/scratch/stefan/7769621/working/3D/196' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=NC=CC=C1Cl)

`REAL300000040136.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040136.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040136/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040136 none CC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=NC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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]
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, 30, 30, 30, 23, 7, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 23, 23, 23, 23, 1, 1, 1] 30
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 88
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040136 none CC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=NC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 24, 24, 30, 30, 30, 30, 30, 30, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 30, 30, 30] 30
rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 10, 24, 25, 26] set([6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 61
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040136 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040136/1 /scratch/stefan/7769621/working/building/REAL300000040136 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 197)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/197
`/scratch/stefan/7769621/working/3D/197' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NC=CC=C1Cl)C1=CC(C(=O)[O-])=CC=C1C)

`REAL300000040136.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040136.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040136/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040136 none CC(=NNC1=NC=CC=C1Cl)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 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
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [10, 1, 10, 10, 34, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 10, 10, 10, 34, 50, 50, 50, 1, 1, 1, 2, 2, 2] 50
rigid atoms, others: [1, 11, 12, 13, 14, 17, 18, 19, 20, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33])
total number of confs: 117
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040136 none CC(=NNC1=NC=CC=C1Cl)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 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
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [27, 27, 11, 1, 1, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 11, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33])
total number of confs: 92
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040136 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040136
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040136/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040136/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040136
Building REAL300000040137
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040137'
/scratch/stefan/7769621/working/building/REAL300000040137 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040137

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040137/0 /scratch/stefan/7769621/working/building/REAL300000040137 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 198)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/198
`/scratch/stefan/7769621/working/3D/198' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=C(CN=NC2=NC=CC=C2Cl)C=C1)C(=O)[O-])

`REAL300000040137.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040137.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040137/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040137 none CC(OC1=CC=C(CN=NC2=NC=CC=C2Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 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, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 137, 64, 16, 64, 64, 12, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 63, 64, 201, 201, 201, 201, 201, 201, 201, 64, 64, 12, 12, 1, 1, 1, 63, 64] 201
rigid atoms, others: [32, 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, 33, 34])
total number of confs: 701
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040137 none CC(OC1=CC=C(CN=NC2=NC=CC=C2Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 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, 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
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, 8, 61, 61, 63, 63, 63, 63, 63, 63, 1, 1, 14, 20, 20, 14, 14, 14, 14, 1, 1, 8, 8, 63, 63, 63, 1, 1] 201
rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 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])
total number of confs: 153
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040137 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040137
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040137/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040137
Building REAL300000040138
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040138'
/scratch/stefan/7769621/working/building/REAL300000040138 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040138

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040138/0 /scratch/stefan/7769621/working/building/REAL300000040138 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 199)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/199
`/scratch/stefan/7769621/working/3D/199' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1CCC(N=NC2=NC=CC=C2Cl)C2=CC=CC=C21)

`REAL300000040138.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040138.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040138/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040138 none O=C([O-])C1CCC(N=NC2=NC=CC=C2Cl)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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: [11, 1, 11, 5, 5, 5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 9, 9, 9, 9] 9
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 18
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040138 none O=C([O-])C1CCC(N=NC2=NC=CC=C2Cl)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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: [11, 1, 11, 5, 5, 5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 1, 1, 1, 1] 9
rigid atoms, others: [1, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30])
total number of confs: 17
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040138 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040138
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040138/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040138
Building REAL300000040139
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040139'
/scratch/stefan/7769621/working/building/REAL300000040139 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040139

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040139/0 /scratch/stefan/7769621/working/building/REAL300000040139 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 200)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/200
`/scratch/stefan/7769621/working/3D/200' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CN1C=C(CN=NC2=NC=CC=C2Cl)C2=CC=CC=C21)

`REAL300000040139.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040139.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040139/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040139 none O=C([O-])CN1C=C(CN=NC2=NC=CC=C2Cl)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 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, 7, 7, 7, 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, 87, 87, 87, 25, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 87, 87, 87, 201, 201, 87, 24, 24, 1, 1, 1, 87, 87, 87, 87] 201
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 685
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040139 none O=C([O-])CN1C=C(CN=NC2=NC=CC=C2Cl)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 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, 7, 7, 7, 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: [14, 8, 14, 1, 1, 1, 1, 1, 9, 64, 65, 87, 87, 87, 87, 87, 87, 1, 1, 1, 1, 1, 1, 8, 8, 1, 9, 9, 87, 87, 87, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 25, 31] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 26, 27, 28, 29, 30])
total number of confs: 182
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040139 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040139
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040139/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040139
Building REAL300000040140
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040140'
/scratch/stefan/7769621/working/building/REAL300000040140 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040140

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040140/0 /scratch/stefan/7769621/working/building/REAL300000040140 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 201)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/201
`/scratch/stefan/7769621/working/3D/201' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=NC=CC=C1Cl)C1=CC=CC(OCCCC(=O)[O-])=C1)

`REAL300000040140.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040140.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040140/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040140 none CC(N=NC1=NC=CC=C1Cl)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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]
dock color type numbers: [7, 7, 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]
0  hydrogens 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, 27, 27, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 6, 17, 20, 36, 57, 57, 1, 7, 7, 7, 7, 29, 29, 29, 1, 1, 1, 17, 17, 20, 20, 37, 37, 1] 201
rigid atoms, others: [32, 1, 33, 40, 11, 12, 13, 14, 15, 16, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39])
total number of confs: 283
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040140 none CC(N=NC1=NC=CC=C1Cl)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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]
dock color type numbers: [7, 7, 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]
0  hydrogens 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, 2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 29, 29, 29, 29, 29, 113, 140, 142, 201, 201, 201, 29, 9, 9, 9, 9, 1, 1, 1, 29, 29, 29, 140, 140, 142, 142, 201, 201, 29] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 648
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040140 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040140/1 /scratch/stefan/7769621/working/building/REAL300000040140 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 202)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/202
`/scratch/stefan/7769621/working/3D/202' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NC=CC=C1Cl)C1=CC=CC(OCCCC(=O)[O-])=C1)

`REAL300000040140.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040140.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040140/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040140 none CC(=NNC1=NC=CC=C1Cl)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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]
dock color type numbers: [7, 7, 7, 4, 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]
0  hydrogens 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, 19, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 6, 22, 39, 63, 83, 83, 1, 9, 9, 9, 19, 28, 28, 28, 1, 1, 1, 22, 22, 38, 38, 63, 63, 1] 201
rigid atoms, others: [32, 1, 33, 40, 11, 12, 13, 14, 15, 16, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39])
total number of confs: 409
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040140 none CC(=NNC1=NC=CC=C1Cl)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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]
dock color type numbers: [7, 7, 7, 4, 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]
0  hydrogens 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, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 28, 28, 28, 28, 28, 86, 125, 159, 201, 201, 201, 28, 8, 8, 8, 4, 1, 1, 1, 28, 28, 28, 125, 125, 159, 159, 201, 201, 28] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 721
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040140 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040140
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040140/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040140/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040140
Building REAL300000040141
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040141'
/scratch/stefan/7769621/working/building/REAL300000040141 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040141

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040141/0 /scratch/stefan/7769621/working/building/REAL300000040141 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 203)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/203
`/scratch/stefan/7769621/working/3D/203' -> `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=NC1=NC=CC=C1Cl)

`REAL300000040141.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040141.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040141/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040141 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=NC=CC=C1Cl 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.ar', 'N.ar', 'C.ar', '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, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 19, 45, 50, 50, 50, 50, 50, 168, 201, 201, 201, 201, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 48, 48, 49, 50, 50, 50, 201, 201, 201, 201, 50, 50, 1, 1, 1] 201
rigid atoms, others: [41, 42, 43, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 557
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040141 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=NC=CC=C1Cl 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.ar', 'N.ar', 'C.ar', '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, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 2, 1, 1, 1, 1, 1, 1, 11, 28, 28, 41, 41, 1, 1, 8, 41, 41, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 3, 3, 2, 2, 1, 1, 28, 28, 28, 28, 1, 1, 50, 50, 50] 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])
total number of confs: 220
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040141 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040141
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040141/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040141
Building REAL300000040142
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040142'
/scratch/stefan/7769621/working/building/REAL300000040142 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040142

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040142/0 /scratch/stefan/7769621/working/building/REAL300000040142 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 204)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/204
`/scratch/stefan/7769621/working/3D/204' -> `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=NC1=NC=CC=C1Cl)

`REAL300000040142.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040142.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040142/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040142 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=NC=CC=C1Cl 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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', '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, 1, 8, 1, 1, 1, 1, 16, 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, 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: [19, 3, 19, 51, 59, 63, 63, 59, 63, 156, 201, 201, 201, 63, 63, 3, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 56, 56, 57, 59, 63, 63, 201, 201, 63, 63, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 639
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040142 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=NC=CC=C1Cl 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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', '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, 1, 8, 1, 1, 1, 1, 16, 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, 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, 5, 4, 1, 1, 1, 1, 1, 1, 6, 23, 38, 38, 1, 1, 11, 53, 53, 63, 63, 63, 63, 63, 63, 11, 11, 11, 11, 5, 5, 4, 4, 1, 1, 23, 23, 1, 1, 63, 63, 63] 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])
total number of confs: 229
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040142 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040142
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040142/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040142
Building REAL300000040143
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040143'
/scratch/stefan/7769621/working/building/REAL300000040143 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040143

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040143/0 /scratch/stefan/7769621/working/building/REAL300000040143 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 205)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/205
`/scratch/stefan/7769621/working/3D/205' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=NC=CC=C1Cl)C1=CC=CC(OC(C)C(=O)[O-])=C1)

`REAL300000040143.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040143.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040143/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040143 none CC(N=NC1=NC=CC=C1Cl)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 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, 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: [7, 1, 7, 35, 35, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 10, 25, 25, 38, 38, 1, 7, 7, 7, 7, 43, 43, 43, 1, 1, 1, 25, 25, 25, 25, 1] 201
rigid atoms, others: [32, 1, 37, 11, 12, 13, 14, 15, 16, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 196
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040143 none CC(N=NC1=NC=CC=C1Cl)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 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, 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: [15, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 15, 43, 43, 43, 43, 43, 149, 201, 201, 201, 201, 43, 15, 15, 15, 15, 1, 1, 1, 43, 43, 43, 201, 201, 201, 201, 43] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 520
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040143 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040143/1 /scratch/stefan/7769621/working/building/REAL300000040143 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 206)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/206
`/scratch/stefan/7769621/working/3D/206' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NC=CC=C1Cl)C1=CC=CC(OC(C)C(=O)[O-])=C1)

`REAL300000040143.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040143.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040143/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040143 none CC(=NNC1=NC=CC=C1Cl)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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]
dock color type numbers: [7, 7, 7, 4, 7, 3, 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: [9, 1, 9, 9, 30, 62, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 1, 11, 27, 27, 40, 40, 1, 9, 9, 9, 30, 62, 62, 62, 1, 1, 1, 27, 27, 27, 27, 1] 201
rigid atoms, others: [32, 1, 37, 11, 12, 13, 14, 15, 16, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 256
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040143 none CC(=NNC1=NC=CC=C1Cl)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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]
dock color type numbers: [7, 7, 7, 4, 7, 3, 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: [23, 24, 6, 1, 1, 1, 1, 1, 1, 1, 1, 24, 62, 62, 62, 62, 62, 169, 201, 201, 201, 201, 62, 24, 24, 24, 6, 1, 1, 1, 62, 62, 62, 201, 201, 201, 201, 62] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 430
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040143 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040143
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040143/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040143/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040143
Building REAL300000040144
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040144'
/scratch/stefan/7769621/working/building/REAL300000040144 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040144

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040144/0 /scratch/stefan/7769621/working/building/REAL300000040144 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 207)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/207
`/scratch/stefan/7769621/working/3D/207' -> `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=NC1=NC=CC=C1Cl)

`REAL300000040144.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040144.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040144/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040144 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=NC=CC=C1Cl 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.ar', 'N.ar', 'C.ar', '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, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 22, 48, 54, 58, 58, 54, 58, 187, 201, 201, 201, 200, 58, 58, 3, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 51, 51, 53, 54, 58, 58, 201, 201, 201, 201, 58, 58, 1, 1, 1] 201
rigid atoms, others: [41, 42, 43, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 486
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040144 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=NC=CC=C1Cl 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.ar', 'N.ar', 'C.ar', '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, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 5, 4, 1, 1, 1, 1, 1, 1, 6, 19, 19, 31, 28, 1, 1, 11, 48, 48, 58, 58, 58, 58, 58, 58, 11, 11, 11, 11, 5, 5, 4, 4, 1, 1, 19, 19, 19, 19, 1, 1, 58, 58, 58] 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])
total number of confs: 200
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040144 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040144
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040144/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040144
Building REAL300000040145
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040145'
/scratch/stefan/7769621/working/building/REAL300000040145 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040145

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040145/0 /scratch/stefan/7769621/working/building/REAL300000040145 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 208)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/208
`/scratch/stefan/7769621/working/3D/208' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(N=NC1=NC=CC=C1Cl)C1=CC=C(OCCCCC(=O)[O-])C=C1)

`REAL300000040145.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040145.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040145/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040145 none CCC(N=NC1=NC=CC=C1Cl)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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]
dock color type numbers: [7, 7, 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]
0  hydrogens 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, 1, 4, 13, 13, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 6, 10, 27, 38, 64, 79, 83, 1, 1, 5, 5, 5, 5, 5, 4, 16, 16, 16, 1, 1, 10, 10, 27, 27, 39, 39, 63, 63, 1, 1] 201
rigid atoms, others: [2, 35, 36, 45, 12, 13, 14, 15, 16, 46, 24, 25] 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, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 399
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040145 none CCC(N=NC1=NC=CC=C1Cl)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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]
dock color type numbers: [7, 7, 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]
0  hydrogens 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, 10, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 10, 16, 16, 10, 14, 60, 70, 118, 147, 190, 199, 201, 16, 16, 14, 14, 14, 14, 14, 10, 1, 1, 1, 16, 16, 70, 70, 118, 118, 147, 147, 190, 190, 16, 16] 201
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 849
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040145 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040145
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040145/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040145
Building REAL300000040146
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040146'
/scratch/stefan/7769621/working/building/REAL300000040146 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040146

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040146/0 /scratch/stefan/7769621/working/building/REAL300000040146 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 209)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/209
`/scratch/stefan/7769621/working/3D/209' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=NC=CC=C2Cl)C1)

`REAL300000040146.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040146.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040146/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040146 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=NC=CC=C2Cl)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.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', '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, 5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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, 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
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [17, 17, 17, 17, 17, 19, 19, 19, 19, 19, 17, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 19, 19, 19, 19, 19, 17, 17, 17, 1, 1, 1, 17, 17] 19
rigid atoms, others: [32, 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, 33, 34])
total number of confs: 41
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: REAL300000040146 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=NC=CC=C2Cl)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.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', '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, 5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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, 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
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [6, 5, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 19, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 5, 5] 19
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 35
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040146 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=NC=CC=C2Cl)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.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', '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, 5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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, 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
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 5, 5, 1, 5, 5, 1, 1, 1, 9, 9, 17, 17, 17, 17, 17, 17, 1, 5, 5, 3, 5, 5, 1, 1, 1, 17, 17, 17, 1, 1] 19
rigid atoms, others: [1, 34, 3, 4, 33, 10, 11, 12, 21, 27, 28, 29] set([0, 2, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32])
total number of confs: 42
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040146 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040146
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040146/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040146
Building REAL300000040147
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040147'
/scratch/stefan/7769621/working/building/REAL300000040147 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040147

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040147/0 /scratch/stefan/7769621/working/building/REAL300000040147 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 210)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/210
`/scratch/stefan/7769621/working/3D/210' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=NC=CC=C1Cl)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C)

`REAL300000040147.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040147.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040147/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040147 none CC(N=NC1=NC=CC=C1Cl)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 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, 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]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 19, 19, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 7, 12, 12, 1, 1, 1, 4, 4, 4, 4, 29, 29, 29, 1, 1, 7, 7, 2, 2, 2, 2, 2, 2] 40
rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 97
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040147 none CC(N=NC1=NC=CC=C1Cl)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 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, 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]
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: [20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 20, 29, 29, 29, 29, 29, 40, 40, 40, 29, 29, 29, 20, 20, 20, 20, 1, 1, 1, 29, 29, 40, 40, 29, 29, 29, 29, 29, 29] 40
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 152
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040147 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040147
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040147/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040147
Building REAL300000040148
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040148'
/scratch/stefan/7769621/working/building/REAL300000040148 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040148

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040148/0 /scratch/stefan/7769621/working/building/REAL300000040148 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 211)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/211
`/scratch/stefan/7769621/working/3D/211' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(N=NC2=NC=CC=C2Cl)CCC(C(=O)[O-])C1(C)C)

`REAL300000040148.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040148.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040148/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040148 none CC1C(N=NC2=NC=CC=C2Cl)CCC(C(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.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, 8, 1, 1, 1, 1, 16, 5, 5, 5, 1, 11, 11, 5, 5, 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, 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]
0  hydrogens need rotated
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [12, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 12
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 25
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040148 none CC1C(N=NC2=NC=CC=C2Cl)CCC(C(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.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, 8, 1, 1, 1, 1, 16, 5, 5, 5, 1, 11, 11, 5, 5, 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, 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]
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: [1, 1, 1, 1, 8, 8, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 3, 3, 1, 1, 1, 2, 2, 2, 1, 1, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 12
rigid atoms, others: [0, 1, 2, 3, 36, 33, 35, 32, 12, 13, 14, 15, 34, 18, 19, 20, 24, 25, 29, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 38, 16, 17, 21, 22, 23, 39, 26, 27, 28, 37])
total number of confs: 33
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040148 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040148
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040148/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040148
Building REAL300000040149
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040149'
/scratch/stefan/7769621/working/building/REAL300000040149 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040149

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040149/0 /scratch/stefan/7769621/working/building/REAL300000040149 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 212)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/212
`/scratch/stefan/7769621/working/3D/212' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(C)N=NC2=NC=CC=C2Cl)=CC=C1OCCCC(=O)[O-])

`REAL300000040149.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040149.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040149/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040149 none COC1=CC(C(C)N=NC2=NC=CC=C2Cl)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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]
dock color type numbers: [7, 3, 7, 7, 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]
0  hydrogens 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, 30, 30, 30, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 102, 156, 159, 201, 201, 201, 52, 52, 52, 30, 7, 7, 7, 7, 1, 1, 1, 30, 30, 156, 156, 159, 159, 201, 201] 201
rigid atoms, others: [34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 6, 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: 721
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040149 none COC1=CC(C(C)N=NC2=NC=CC=C2Cl)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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]
dock color type numbers: [7, 3, 7, 7, 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]
0  hydrogens 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, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 7, 17, 20, 33, 42, 42, 3, 3, 3, 1, 7, 7, 7, 7, 30, 30, 30, 1, 1, 17, 17, 20, 20, 33, 33] 201
rigid atoms, others: [1, 2, 3, 4, 5, 38, 16, 17, 18, 19, 29, 37] 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, 39, 40, 41, 42, 43, 44])
total number of confs: 238
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040149 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040149/1 /scratch/stefan/7769621/working/building/REAL300000040149 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 213)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/213
`/scratch/stefan/7769621/working/3D/213' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(C)=NNC2=NC=CC=C2Cl)=CC=C1OCCCC(=O)[O-])

`REAL300000040149.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040149.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040149/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040149 none COC1=CC(C(C)=NNC2=NC=CC=C2Cl)=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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 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]
0  hydrogens 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, 48, 48, 48, 15, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 115, 176, 180, 201, 201, 201, 75, 75, 75, 48, 15, 15, 15, 3, 1, 1, 1, 48, 48, 176, 176, 180, 180, 201, 201] 201
rigid atoms, others: [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, 33, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 667
number of broken/clashed sets: 83
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040149 none COC1=CC(C(C)=NNC2=NC=CC=C2Cl)=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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 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]
0  hydrogens 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, 29, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 7, 21, 23, 33, 48, 48, 3, 3, 3, 1, 7, 7, 7, 29, 48, 48, 48, 1, 1, 21, 21, 23, 23, 33, 33] 201
rigid atoms, others: [1, 2, 3, 4, 5, 38, 16, 17, 18, 19, 29, 37] 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, 39, 40, 41, 42, 43, 44])
total number of confs: 305
number of broken/clashed sets: 83
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040149 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040149
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040149/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040149/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040149
Building REAL300000040150
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040150'
/scratch/stefan/7769621/working/building/REAL300000040150 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040150

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040150/0 /scratch/stefan/7769621/working/building/REAL300000040150 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 214)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/214
`/scratch/stefan/7769621/working/3D/214' -> `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(N=NC2=NC=CC=C2Cl)C1)

`REAL300000040150.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040150.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040150/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040150 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=NC=CC=C2Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [20, 17, 20, 17, 17, 40, 40, 40, 40, 40, 40, 17, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 40, 40, 40, 40, 17, 17, 17, 1, 1, 1, 17, 17] 40
rigid atoms, others: [32, 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, 33, 34])
total number of confs: 86
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: REAL300000040150 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=NC=CC=C2Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [15, 11, 15, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 26, 26, 40, 40, 40, 40, 40, 40, 11, 1, 1, 1, 1, 11, 11, 11, 40, 40, 40, 11, 11] 40
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 82
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040150 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=NC=CC=C2Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 11, 11, 11, 11, 11, 11, 1, 1, 1, 8, 8, 17, 16, 17, 17, 17, 17, 1, 11, 11, 11, 11, 1, 1, 1, 17, 17, 17, 1, 1] 40
rigid atoms, others: [1, 34, 3, 4, 33, 11, 12, 13, 22, 27, 28, 29] set([0, 2, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 30, 31, 32])
total number of confs: 43
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040150 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040150
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040150/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040150
Building REAL300000040151
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040151'
/scratch/stefan/7769621/working/building/REAL300000040151 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040151

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040151/0 /scratch/stefan/7769621/working/building/REAL300000040151 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 215)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/215
`/scratch/stefan/7769621/working/3D/215' -> `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(N=NC2=NC=CC=C2Cl)C1)

`REAL300000040151.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040151.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040151/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040151 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(N=NC2=NC=CC=C2Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 5, 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, 3, 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: [20, 17, 20, 17, 17, 41, 41, 41, 41, 41, 41, 17, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 41, 41, 41, 41, 17, 17, 17, 1, 1, 1, 17, 17] 41
rigid atoms, others: [32, 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, 33, 34])
total number of confs: 87
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: REAL300000040151 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(N=NC2=NC=CC=C2Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [15, 11, 15, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 27, 27, 41, 41, 41, 41, 41, 41, 11, 1, 1, 1, 1, 11, 11, 11, 41, 41, 41, 11, 11] 41
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 84
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040151 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(N=NC2=NC=CC=C2Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 5, 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, 3, 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: [3, 1, 3, 1, 1, 11, 11, 11, 11, 11, 11, 1, 1, 1, 8, 8, 17, 16, 17, 17, 17, 17, 1, 11, 11, 11, 11, 1, 1, 1, 17, 17, 17, 1, 1] 41
rigid atoms, others: [1, 34, 3, 4, 33, 11, 12, 13, 22, 27, 28, 29] set([0, 2, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 30, 31, 32])
total number of confs: 43
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040151 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040151
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040151/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040151
Building REAL300000040152
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040152'
/scratch/stefan/7769621/working/building/REAL300000040152 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040152

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040152/0 /scratch/stefan/7769621/working/building/REAL300000040152 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 216)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/216
`/scratch/stefan/7769621/working/3D/216' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(=C1)CCCC2N=NC1=NC=CC=C1Cl)

`REAL300000040152.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040152.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040152/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040152 none O=C([O-])C1=CC=C2C(=C1)CCCC2N=NC1=NC=CC=C1Cl 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', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1] 9
rigid atoms, others: [32, 33, 34, 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])
total number of confs: 18
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040152 none O=C([O-])C1=CC=C2C(=C1)CCCC2N=NC1=NC=CC=C1Cl 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', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9] 9
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 21])
total number of confs: 12
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040152 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040152/1 /scratch/stefan/7769621/working/building/REAL300000040152 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 217)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/217
`/scratch/stefan/7769621/working/3D/217' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC1=NC=CC=C1Cl)

`REAL300000040152.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040152.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040152/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040152 none O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC1=NC=CC=C1Cl 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', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1] 17
rigid atoms, others: [32, 33, 34, 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])
total number of confs: 28
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040152 none O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC1=NC=CC=C1Cl 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', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17] 17
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([32, 33, 34, 15, 16, 17, 18, 19, 20, 21, 31])
total number of confs: 27
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040152 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040152
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040152/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040152/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040152
Building REAL300000040153
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040153'
/scratch/stefan/7769621/working/building/REAL300000040153 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040153

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040153/0 /scratch/stefan/7769621/working/building/REAL300000040153 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 218)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/218
`/scratch/stefan/7769621/working/3D/218' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=NC=CC=C1Cl)C1=CC(Br)=CC=C1OCC(=O)[O-])

`REAL300000040153.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040153.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040153/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040153 none CC(N=NC1=NC=CC=C1Cl)C1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 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, 7, 7, 7, 3, 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: [6, 1, 6, 31, 31, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 7, 36, 71, 71, 6, 6, 6, 6, 53, 53, 53, 1, 1, 1, 36, 36] 201
rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 310
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040153 none CC(N=NC1=NC=CC=C1Cl)C1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 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, 7, 7, 7, 3, 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: [29, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 29, 53, 53, 53, 29, 53, 53, 53, 131, 201, 201, 201, 29, 29, 29, 29, 1, 1, 1, 53, 53, 53, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34])
total number of confs: 687
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040153 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040153
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040153/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040153
Building REAL300000040154
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040154'
/scratch/stefan/7769621/working/building/REAL300000040154 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040154

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040154/0 /scratch/stefan/7769621/working/building/REAL300000040154 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 219)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/219
`/scratch/stefan/7769621/working/3D/219' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C2C(=C1)OC(C(C)N=NC1=NC=CC=C1Cl)=C2CC(=O)[O-])

`REAL300000040154.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040154.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040154/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040154 none CC1=CC=C2C(=C1)OC(C(C)N=NC1=NC=CC=C1Cl)=C2CC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 5, 1, 11, 11, 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, 3, 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
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [58, 58, 58, 58, 58, 58, 58, 58, 30, 7, 30, 7, 1, 1, 1, 1, 1, 1, 1, 1, 58, 58, 66, 66, 66, 58, 58, 58, 58, 58, 58, 30, 30, 30, 30, 1, 1, 1, 66, 66] 66
rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39])
total number of confs: 186
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040154 none CC1=CC=C2C(=C1)OC(C(C)N=NC1=NC=CC=C1Cl)=C2CC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 5, 1, 11, 11, 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, 3, 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
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 41, 41, 58, 58, 58, 58, 58, 58, 1, 1, 3, 7, 7, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 58, 58, 58, 3, 3] 66
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 28, 29, 30] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 114
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040154 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040154
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040154/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040154
Building REAL300000040155
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040155'
/scratch/stefan/7769621/working/building/REAL300000040155 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040155

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040155/0 /scratch/stefan/7769621/working/building/REAL300000040155 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 220)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/220
`/scratch/stefan/7769621/working/3D/220' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1CN=NC1=NC=CC=C1Cl)

`REAL300000040155.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040155.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040155/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040155 none CC1=CC(C)=C(C(=O)[O-])C=C1CN=NC1=NC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46, 46, 46, 24, 24, 1, 1, 1] 46
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 116
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040155 none CC1=CC(C)=C(C(=O)[O-])C=C1CN=NC1=NC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 8, 42, 42, 46, 46, 46, 46, 46, 46, 2, 2, 2, 1, 2, 2, 2, 1, 8, 8, 46, 46, 46] 46
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 24, 28] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33])
total number of confs: 90
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040155 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040155/1 /scratch/stefan/7769621/working/building/REAL300000040155 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 221)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/221
`/scratch/stefan/7769621/working/3D/221' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=NC=CC=C1Cl)

`REAL300000040155.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040155.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040155/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040155 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=NC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 46, 46, 11, 1, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 78, 78, 78, 78, 46, 11, 1, 1, 1] 78
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 126
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040155 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=NC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 10, 10, 44, 78, 78, 78, 78, 78, 78, 2, 2, 2, 1, 2, 2, 2, 1, 10, 44, 78, 78, 78] 78
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 24, 28] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33])
total number of confs: 172
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040155 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040155
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040155/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040155/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040155
Building REAL300000040156
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040156'
/scratch/stefan/7769621/working/building/REAL300000040156 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040156

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040156/0 /scratch/stefan/7769621/working/building/REAL300000040156 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 222)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/222
`/scratch/stefan/7769621/working/3D/222' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(C=NNC2=NC=CC=C2Cl)=C1Cl)

`REAL300000040156.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040156.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040156/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040156 none O=C([O-])C1=CC=CC(C=NNC2=NC=CC=C2Cl)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 34, 33, 9, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 33, 9, 1, 1, 1] 42
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24])
total number of confs: 68
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040156 none O=C([O-])C1=CC=CC(C=NNC2=NC=CC=C2Cl)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 22, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 1, 6, 22, 42, 42, 42] 42
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27])
total number of confs: 88
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040156 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040156
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040156/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040156
Building REAL300000040157
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040157'
/scratch/stefan/7769621/working/building/REAL300000040157 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040157

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040157/0 /scratch/stefan/7769621/working/building/REAL300000040157 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 223)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/223
`/scratch/stefan/7769621/working/3D/223' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(=C1)CCCCC2N=NC1=NC=CC=C1Cl)

`REAL300000040157.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040157.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040157/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040157 none O=C([O-])C1=CC=C2C(=C1)CCCCC2N=NC1=NC=CC=C1Cl 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
6  conformations in input
total number of sets (complete confs): 6
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1] 6
rigid atoms, others: [35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 10
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040157 none O=C([O-])C1=CC=C2C(=C1)CCCCC2N=NC1=NC=CC=C1Cl 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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6] 6
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34] set([35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 22])
total number of confs: 9
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040157 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040157/1 /scratch/stefan/7769621/working/building/REAL300000040157 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 224)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/224
`/scratch/stefan/7769621/working/3D/224' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC1=NC=CC=C1Cl)

`REAL300000040157.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040157.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040157/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040157 none O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC1=NC=CC=C1Cl 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', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 16, 16, 16, 16, 16, 16, 16, 16, 17, 16, 16, 9, 1, 1, 1, 1, 1, 1, 1, 1, 17, 16, 16, 17, 16, 16, 17, 17, 17, 16, 17, 9, 1, 1, 1] 17
rigid atoms, others: [35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 43
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040157 none O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC1=NC=CC=C1Cl 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', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 16, 16, 16] 17
rigid atoms, others: [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] set([34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 22])
total number of confs: 30
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040157 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040157
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040157/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040157/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040157
Building REAL300000040158
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040158'
/scratch/stefan/7769621/working/building/REAL300000040158 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040158

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040158/0 /scratch/stefan/7769621/working/building/REAL300000040158 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 225)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/225
`/scratch/stefan/7769621/working/3D/225' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C(OC1=CC=CC(CN=NC2=NC=CC=C2Cl)=C1)C1=CC=CC=C1)

`REAL300000040158.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040158.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040158/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040158 none O=C([O-])C(OC1=CC=CC(CN=NC2=NC=CC=C2Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 22, 22, 22, 22, 22, 82, 201, 201, 201, 201, 201, 201, 201, 201, 22, 1, 1, 1, 1, 1, 1, 3, 22, 22, 22, 82, 82, 201, 201, 201, 22, 1, 1, 1, 1, 1] 201
rigid atoms, others: [3, 37, 38, 39, 40, 41, 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, 36])
total number of confs: 456
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: REAL300000040158 none O=C([O-])C(OC1=CC=CC(CN=NC2=NC=CC=C2Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 123, 41, 41, 41, 41, 41, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 201, 201, 201, 201, 201, 201, 201, 41, 41, 41, 9, 9, 1, 1, 1, 41, 201, 201, 201, 201, 201] 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, 40, 41])
total number of confs: 577
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040158 none O=C([O-])C(OC1=CC=CC(CN=NC2=NC=CC=C2Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 21, 22, 9, 1, 1, 1, 1, 1, 1, 1, 8, 41, 41, 41, 41, 41, 41, 41, 41, 1, 21, 22, 22, 21, 22, 22, 21, 1, 1, 1, 8, 8, 41, 41, 41, 1, 22, 22, 21, 22, 22] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 20, 36, 28, 29, 30] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41])
total number of confs: 136
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040158 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040158
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040158/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040158
Building REAL300000040159
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040159'
/scratch/stefan/7769621/working/building/REAL300000040159 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040159

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040159/0 /scratch/stefan/7769621/working/building/REAL300000040159 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 226)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/226
`/scratch/stefan/7769621/working/3D/226' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)OC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=NC=CC=C1Cl)

`REAL300000040159.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040159.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040159/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040159 none CC(C)OC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=NC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 11, 11, 1, 1, 5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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, 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]
0  hydrogens need rotated
155  conformations in input
total number of sets (complete confs): 155
using faster count positions algorithm for large data
unique positions, atoms: [155, 155, 155, 102, 102, 102, 102, 102, 102, 102, 102, 102, 38, 6, 38, 6, 1, 1, 1, 1, 1, 1, 1, 1, 155, 155, 155, 155, 155, 155, 155, 102, 102, 102, 38, 38, 38, 38, 1, 1, 1] 155
rigid atoms, others: [38, 39, 40, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 307
number of broken/clashed sets: 34
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040159 none CC(C)OC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=NC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 11, 11, 1, 1, 5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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, 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]
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: [18, 8, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 55, 55, 102, 102, 102, 102, 102, 102, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 8, 8, 8, 8, 102, 102, 102] 155
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 31] set([0, 1, 2, 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: 210
number of broken/clashed sets: 34
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040159 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040159/1 /scratch/stefan/7769621/working/building/REAL300000040159 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 227)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/227
`/scratch/stefan/7769621/working/3D/227' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NC=CC=C1Cl)C1=CC(C(=O)[O-])=CC=C1OC(C)C)

`REAL300000040159.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040159.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040159/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040159 none CC(=NNC1=NC=CC=C1Cl)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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]
0  hydrogens 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, 161, 161, 161, 161, 161, 161, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 15, 15, 9, 9, 9, 55, 161, 161, 161, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15] 201
rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 17, 18, 19, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 328
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040159 none CC(=NNC1=NC=CC=C1Cl)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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]
0  hydrogens 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, 11, 1, 1, 1, 1, 1, 1, 1, 1, 39, 161, 161, 161, 161, 161, 161, 161, 161, 161, 201, 201, 201, 40, 40, 40, 11, 1, 1, 1, 161, 161, 161, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 305
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040159 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040159
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040159/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040159/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040159
Building REAL300000040160
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040160'
/scratch/stefan/7769621/working/building/REAL300000040160 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040160

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040160/0 /scratch/stefan/7769621/working/building/REAL300000040160 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 228)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/228
`/scratch/stefan/7769621/working/3D/228' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC2=C1C(N=NC1=NC=CC=C1Cl)CC2)

`REAL300000040160.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040160.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040160/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040160 none O=C([O-])C1=CC=CC2=C1C(N=NC1=NC=CC=C1Cl)CC2 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', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', '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, 8, 8, 1, 8, 1, 1, 1, 1, 16, 5, 5, 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]
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, 17, 17, 17, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 17, 17, 17, 17] 17
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31])
total number of confs: 32
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040160 none O=C([O-])C1=CC=CC2=C1C(N=NC1=NC=CC=C1Cl)CC2 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', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', '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, 8, 8, 1, 8, 1, 1, 1, 1, 16, 5, 5, 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]
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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 17, 17, 17, 1, 1, 1, 1] 17
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27])
total number of confs: 29
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040160 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040160/1 /scratch/stefan/7769621/working/building/REAL300000040160 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 229)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/229
`/scratch/stefan/7769621/working/3D/229' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC2=C1C(=NNC1=NC=CC=C1Cl)CC2)

`REAL300000040160.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040160.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040160/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040160 none O=C([O-])C1=CC=CC2=C1C(=NNC1=NC=CC=C1Cl)CC2 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.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', '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, 8, 8, 1, 8, 1, 1, 1, 1, 16, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 21, 11, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 22, 22, 22, 11, 1, 1, 1, 21, 21, 21, 21] 22
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31])
total number of confs: 41
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040160 none O=C([O-])C1=CC=CC2=C1C(=NNC1=NC=CC=C1Cl)CC2 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.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', '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, 8, 8, 1, 8, 1, 1, 1, 1, 16, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 21, 21, 22, 1, 1, 1, 1, 1, 9, 21, 21, 22, 1, 1, 1, 1] 22
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 28, 29, 30, 31] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27])
total number of confs: 46
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040160 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040160
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040160/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040160/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040160
Building REAL300000040161
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040161'
/scratch/stefan/7769621/working/building/REAL300000040161 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040161

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040161/0 /scratch/stefan/7769621/working/building/REAL300000040161 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 230)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/230
`/scratch/stefan/7769621/working/3D/230' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=NC=CC=C3Cl)C=C2)C=C1)

`REAL300000040161.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040161.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040161/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040161 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=NC=CC=C3Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7, 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
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [77, 56, 77, 56, 77, 77, 56, 48, 56, 56, 33, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 56, 56, 77, 77, 77, 77, 56, 56, 33, 33, 1, 1, 1, 56, 56, 77, 77] 77
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37])
total number of confs: 379
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: REAL300000040161 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=NC=CC=C3Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7, 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
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 6, 31, 31, 56, 56, 56, 56, 56, 56, 1, 1, 3, 3, 3, 3, 1, 1, 6, 6, 56, 56, 56, 1, 1, 3, 3] 77
rigid atoms, others: [34, 6, 7, 8, 9, 10, 11, 35, 21, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 29, 30, 31, 32, 33, 36, 37])
total number of confs: 104
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040161 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=NC=CC=C3Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7, 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
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 11, 56, 56, 77, 77, 77, 77, 77, 77, 3, 3, 1, 1, 1, 1, 3, 3, 11, 11, 77, 77, 77, 3, 3, 1, 1] 77
rigid atoms, others: [1, 3, 4, 5, 6, 7, 23, 24, 25, 26, 37, 36] 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])
total number of confs: 141
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040161 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040161
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040161/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040161
Building REAL300000040162
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040162'
/scratch/stefan/7769621/working/building/REAL300000040162 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040162

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040162/0 /scratch/stefan/7769621/working/building/REAL300000040162 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 231)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/231
`/scratch/stefan/7769621/working/3D/231' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2NC=C(CN=NC3=NC=CC=C3Cl)C2=C1)

`REAL300000040162.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040162.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040162/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040162 none O=C([O-])C1=CC=C2NC=C(CN=NC3=NC=CC=C3Cl)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [66, 66, 66, 66, 66, 66, 66, 66, 66, 34, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 66, 34, 34, 1, 1, 1, 66] 66
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 159
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040162 none O=C([O-])C1=CC=C2NC=C(CN=NC3=NC=CC=C3Cl)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 49, 50, 66, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 1, 9, 9, 66, 66, 66, 1] 66
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30])
total number of confs: 110
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040162 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040162
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040162/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040162
Building REAL300000040163
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040163'
/scratch/stefan/7769621/working/building/REAL300000040163 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040163

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040163/0 /scratch/stefan/7769621/working/building/REAL300000040163 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 232)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/232
`/scratch/stefan/7769621/working/3D/232' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(CN=NC2=NC=CC=C2Cl)=CC(Cl)=C1OC(C)C(=O)[O-])

`REAL300000040163.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040163.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040163/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040163 none COC1=CC(CN=NC2=NC=CC=C2Cl)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 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, 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]
0  hydrogens 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, 89, 89, 89, 23, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 89, 89, 181, 201, 201, 201, 201, 133, 133, 133, 89, 22, 22, 1, 1, 1, 89, 201, 201, 201, 201] 201
rigid atoms, others: [32, 33, 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, 34, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040163 none COC1=CC(CN=NC2=NC=CC=C2Cl)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 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, 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]
0  hydrogens 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, 68, 68, 88, 88, 88, 88, 88, 89, 1, 1, 1, 1, 1, 4, 9, 9, 13, 13, 3, 3, 3, 1, 8, 8, 89, 88, 89, 1, 9, 10, 10, 10] 201
rigid atoms, others: [1, 2, 3, 4, 5, 34, 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, 35, 36, 37, 38])
total number of confs: 193
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040163 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040163/1 /scratch/stefan/7769621/working/building/REAL300000040163 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 233)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/233
`/scratch/stefan/7769621/working/3D/233' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=NC=CC=C2Cl)=CC(Cl)=C1OC(C)C(=O)[O-])

`REAL300000040163.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040163.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040163/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040163 none COC1=CC(C=NNC2=NC=CC=C2Cl)=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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 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]
0  hydrogens 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, 80, 80, 80, 27, 27, 5, 1, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 168, 195, 195, 201, 201, 143, 143, 143, 80, 27, 5, 1, 1, 1, 80, 195, 195, 195, 195] 201
rigid atoms, others: [32, 33, 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, 34, 35, 36, 37, 38])
total number of confs: 525
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040163 none COC1=CC(C=NNC2=NC=CC=C2Cl)=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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 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]
0  hydrogens 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, 9, 9, 43, 80, 80, 80, 80, 80, 80, 1, 1, 1, 1, 1, 5, 14, 14, 21, 21, 4, 4, 4, 1, 9, 43, 80, 80, 80, 1, 14, 14, 14, 14] 201
rigid atoms, others: [1, 2, 3, 4, 5, 34, 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, 35, 36, 37, 38])
total number of confs: 239
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040163 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040163
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040163/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040163/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040163
Building REAL300000040164
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040164'
/scratch/stefan/7769621/working/building/REAL300000040164 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040164

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040164/0 /scratch/stefan/7769621/working/building/REAL300000040164 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 234)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/234
`/scratch/stefan/7769621/working/3D/234' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Cl)SC(C=NNC2=NC=CC=C2Cl)=C1)

`REAL300000040164.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040164.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040164/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040164 none O=C([O-])C1=C(Cl)SC(C=NNC2=NC=CC=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
122  conformations in input
total number of sets (complete confs): 122
using faster count positions algorithm for large data
unique positions, atoms: [122, 122, 122, 122, 122, 122, 122, 48, 48, 11, 1, 1, 1, 1, 1, 1, 1, 1, 122, 48, 11, 1, 1, 1, 122] 122
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 24])
total number of confs: 178
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040164 none O=C([O-])C1=C(Cl)SC(C=NNC2=NC=CC=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 13, 13, 50, 122, 122, 122, 122, 122, 122, 1, 13, 50, 122, 122, 122, 1] 122
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 24] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23])
total number of confs: 225
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040164 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040164/1 /scratch/stefan/7769621/working/building/REAL300000040164 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 235)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/235
`/scratch/stefan/7769621/working/3D/235' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Cl)SC(CN=NC2=NC=CC=C2Cl)=C1)

`REAL300000040164.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040164.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040164/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040164 none O=C([O-])C1=C(Cl)SC(CN=NC2=NC=CC=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 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]
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: [152, 153, 153, 153, 153, 153, 153, 53, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 153, 52, 52, 1, 1, 1, 153] 153
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 24])
total number of confs: 295
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040164 none O=C([O-])C1=C(Cl)SC(CN=NC2=NC=CC=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 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]
0  hydrogens need rotated
153  conformations in input
total number of sets (complete confs): 153
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 76, 77, 153, 153, 153, 153, 153, 153, 1, 8, 8, 153, 153, 153, 1] 153
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 24] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23])
total number of confs: 233
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040164 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040164
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040164/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040164/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040164
Building REAL300000040165
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040165'
/scratch/stefan/7769621/working/building/REAL300000040165 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040165

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040165/0 /scratch/stefan/7769621/working/building/REAL300000040165 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 236)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/236
`/scratch/stefan/7769621/working/3D/236' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(=O)[O-])=CC=C1C(C)N=NC1=NC=CC=C1Cl)

`REAL300000040165.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040165.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040165/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040165 none CC1=CC(C(=O)[O-])=CC=C1C(C)N=NC1=NC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [26, 26, 26, 19, 26, 26, 26, 26, 26, 19, 7, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 19, 19, 19, 19, 1, 1, 1] 26
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 102
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040165 none CC1=CC(C(=O)[O-])=CC=C1C(C)N=NC1=NC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 24, 24, 26, 26, 26, 26, 26, 26, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 26, 26, 26] 26
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31])
total number of confs: 49
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040165 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040165/1 /scratch/stefan/7769621/working/building/REAL300000040165 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 237)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/237
`/scratch/stefan/7769621/working/3D/237' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NC=CC=C1Cl)C1=CC=C(C(=O)[O-])C=C1C)

`REAL300000040165.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040165.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040165/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040165 none CC(=NNC1=NC=CC=C1Cl)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 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
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 10, 10, 36, 56, 56, 56, 56, 56, 56, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 10, 10, 10, 36, 56, 56, 56, 1, 1, 1, 2, 2, 2] 56
rigid atoms, others: [1, 11, 12, 13, 14, 15, 18, 19, 20, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33])
total number of confs: 131
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040165 none CC(=NNC1=NC=CC=C1Cl)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 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
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [35, 35, 11, 1, 1, 1, 1, 1, 1, 1, 1, 35, 56, 56, 36, 38, 56, 56, 56, 56, 56, 36, 36, 36, 11, 1, 1, 1, 56, 56, 56, 56, 56, 56] 56
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33])
total number of confs: 216
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040165 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040165
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040165/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040165/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040165
Building REAL300000040166
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040166'
/scratch/stefan/7769621/working/building/REAL300000040166 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040166

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040166/0 /scratch/stefan/7769621/working/building/REAL300000040166 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 238)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/238
`/scratch/stefan/7769621/working/3D/238' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C(Cl)C=C1C=NNC1=NC=CC=C1Cl)

`REAL300000040166.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040166.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040166/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040166 none O=C([O-])C1=CN=C(Cl)C=C1C=NNC1=NC=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 16, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [42, 42, 42, 42, 42, 37, 42, 42, 42, 26, 25, 9, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 25, 9, 1, 1, 1] 42
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23])
total number of confs: 86
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040166 none O=C([O-])C1=CN=C(Cl)C=C1C=NNC1=NC=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 16, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 42, 42, 42, 42, 42, 42, 1, 1, 6, 26, 42, 42, 42] 42
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26])
total number of confs: 94
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040166 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040166
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040166/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040166
Building REAL300000040167
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040167'
/scratch/stefan/7769621/working/building/REAL300000040167 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040167

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040167/0 /scratch/stefan/7769621/working/building/REAL300000040167 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 239)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/239
`/scratch/stefan/7769621/working/3D/239' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C2=CC=C(CN=NC3=NC=CC=C3Cl)O2)=CC=C1O)

`REAL300000040167.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040167.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040167/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040167 none O=C([O-])C1=CC(C2=CC=C(CN=NC3=NC=CC=C3Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 12, 1, 1, 1, 12, 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, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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, 86, 86, 86, 86, 18, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 86, 201, 201, 201, 201, 201, 86, 86, 17, 17, 1, 1, 1, 201, 201, 402] 402
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35])
total number of confs: 702
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: REAL300000040167 none O=C([O-])C1=CC(C2=CC=C(CN=NC3=NC=CC=C3Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 12, 1, 1, 1, 12, 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, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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: [15, 12, 15, 11, 11, 1, 1, 1, 1, 1, 1, 8, 67, 67, 85, 85, 85, 85, 85, 86, 1, 11, 11, 11, 11, 12, 1, 1, 8, 8, 85, 85, 86, 12, 12, 22] 402
rigid atoms, others: [5, 6, 7, 8, 9, 10, 20, 26, 27] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 185
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040167 none O=C([O-])C1=CC(C2=CC=C(CN=NC3=NC=CC=C3Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 12, 1, 1, 1, 12, 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, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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, 11, 11, 11, 12, 56, 197, 197, 201, 201, 201, 201, 201, 201, 11, 1, 1, 1, 1, 1, 12, 11, 55, 56, 201, 201, 201, 1, 1, 2] 402
rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 21, 22, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 35])
total number of confs: 388
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040167 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040167/1 /scratch/stefan/7769621/working/building/REAL300000040167 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 240)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/240
`/scratch/stefan/7769621/working/3D/240' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C2=CC=C(C=NNC3=NC=CC=C3Cl)O2)=CC=C1O)

`REAL300000040167.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040167.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040167/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040167 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=NC=CC=C3Cl)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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 8, 1, 8, 1, 1, 1, 1, 16, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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, 98, 98, 98, 98, 51, 51, 11, 1, 1, 1, 1, 1, 1, 1, 1, 98, 201, 201, 201, 201, 201, 98, 98, 51, 11, 1, 1, 1, 201, 201, 402] 402
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35])
total number of confs: 692
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: REAL300000040167 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=NC=CC=C3Cl)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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 8, 1, 8, 1, 1, 1, 1, 16, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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: [25, 12, 25, 12, 12, 1, 1, 1, 1, 1, 1, 9, 9, 41, 98, 98, 98, 98, 98, 98, 1, 12, 12, 12, 12, 12, 1, 1, 9, 41, 98, 98, 98, 12, 12, 24] 402
rigid atoms, others: [5, 6, 7, 8, 9, 10, 20, 26, 27] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 256
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040167 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=NC=CC=C3Cl)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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 8, 1, 8, 1, 1, 1, 1, 16, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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, 12, 12, 12, 12, 40, 40, 140, 201, 201, 201, 201, 201, 201, 12, 1, 1, 1, 1, 1, 12, 12, 40, 140, 201, 201, 201, 1, 1, 2] 402
rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 21, 22, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 35])
total number of confs: 454
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040167 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040167
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040167/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040167/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040167
Building REAL300000040168
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040168'
/scratch/stefan/7769621/working/building/REAL300000040168 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040168

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040168/0 /scratch/stefan/7769621/working/building/REAL300000040168 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 241)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/241
`/scratch/stefan/7769621/working/3D/241' -> `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=NNC1=NC=CC=C1Cl)

`REAL300000040168.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040168.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040168/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040168 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=NC=CC=C1Cl 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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 19, 19, 10, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 19, 10, 1, 1, 1] 20
rigid atoms, others: [33, 34, 35, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 37
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040168 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=NC=CC=C1Cl 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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 4, 4, 15, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 1, 1, 1, 4, 15, 20, 20, 20] 20
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])
total number of confs: 54
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040168 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040168/1 /scratch/stefan/7769621/working/building/REAL300000040168 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 242)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/242
`/scratch/stefan/7769621/working/3D/242' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC=C(C(=O)[O-])C=C1CN=NC1=NC=CC=C1Cl)

`REAL300000040168.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040168.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040168/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040168 none CN(C)C1=CC=C(C(=O)[O-])C=C1CN=NC1=NC=CC=C1Cl 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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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, 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
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 35, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 64, 64, 64, 64, 64, 35, 35, 1, 1, 1] 64
rigid atoms, others: [33, 34, 35, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 154
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040168 none CN(C)C1=CC=C(C(=O)[O-])C=C1CN=NC1=NC=CC=C1Cl 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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 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, 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
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 42, 42, 64, 64, 64, 64, 64, 64, 4, 4, 4, 4, 4, 4, 1, 1, 1, 8, 8, 64, 64, 64] 64
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30] set([0, 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: 120
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040168 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040168
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040168/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040168/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040168
Building REAL300000040169
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040169'
/scratch/stefan/7769621/working/building/REAL300000040169 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040169

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040169/0 /scratch/stefan/7769621/working/building/REAL300000040169 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 243)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/243
`/scratch/stefan/7769621/working/3D/243' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=NC=CC=C3Cl)S2)C=C1)

`REAL300000040169.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040169.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040169/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040169 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=NC=CC=C3Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 14, 1, 1, 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]
0  hydrogens need 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, 193, 201, 201, 136, 136, 136, 136, 46, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 136, 201, 201, 201, 201, 136, 136, 46, 46, 1, 1, 1, 201, 201] 201
rigid atoms, others: [32, 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, 33, 34])
total number of confs: 434
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: REAL300000040169 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=NC=CC=C3Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 14, 1, 1, 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]
0  hydrogens 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, 8, 77, 77, 135, 135, 135, 135, 135, 136, 1, 7, 7, 7, 7, 1, 1, 8, 8, 135, 135, 136, 7, 7] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 232
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040169 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=NC=CC=C3Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 14, 1, 1, 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]
0  hydrogens 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, 8, 8, 8, 8, 48, 184, 184, 201, 201, 201, 201, 201, 201, 8, 1, 1, 1, 1, 8, 8, 48, 48, 201, 201, 201, 1, 1] 201
rigid atoms, others: [1, 34, 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: 364
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040169 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040169/1 /scratch/stefan/7769621/working/building/REAL300000040169 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 244)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/244
`/scratch/stefan/7769621/working/3D/244' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=NC=CC=C3Cl)S2)C=C1)

`REAL300000040169.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040169.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040169/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040169 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=NC=CC=C3Cl)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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.ar', 'C.ar', '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, 8, 1, 8, 1, 1, 1, 1, 16, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 100, 126, 126, 100, 100, 100, 99, 47, 47, 11, 1, 1, 1, 1, 1, 1, 1, 1, 100, 126, 126, 126, 126, 100, 99, 47, 11, 1, 1, 1, 126, 126] 126
rigid atoms, others: [32, 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, 33, 34])
total number of confs: 327
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: REAL300000040169 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=NC=CC=C3Cl)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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.ar', 'C.ar', '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, 8, 1, 8, 1, 1, 1, 1, 16, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
126  conformations in input
total number of sets (complete confs): 126
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 12, 12, 51, 99, 99, 99, 99, 99, 99, 1, 7, 7, 7, 7, 1, 1, 12, 51, 99, 99, 99, 7, 7] 126
rigid atoms, others: [6, 7, 8, 9, 10, 11, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 224
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040169 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=NC=CC=C3Cl)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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.ar', 'C.ar', '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, 8, 1, 8, 1, 1, 1, 1, 16, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 8, 8, 8, 28, 28, 73, 99, 99, 99, 99, 99, 99, 8, 1, 1, 1, 1, 8, 8, 28, 73, 99, 99, 99, 1, 1] 99
rigid atoms, others: [1, 34, 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: 219
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040169 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040169
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040169/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040169/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040169
Building REAL300000040170
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040170'
/scratch/stefan/7769621/working/building/REAL300000040170 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040170

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040170/0 /scratch/stefan/7769621/working/building/REAL300000040170 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 245)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/245
`/scratch/stefan/7769621/working/3D/245' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(C2=CC=C(CN=NC3=NC=CC=C3Cl)S2)=C1)

`REAL300000040170.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040170.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040170/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040170 none O=C([O-])C1=CC=CC(C2=CC=C(CN=NC3=NC=CC=C3Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.ar', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 14, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 80, 80, 80, 80, 23, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 80, 201, 201, 201, 201, 80, 80, 23, 23, 1, 1, 1, 201] 201
rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 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: 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: REAL300000040170 none O=C([O-])C1=CC=CC(C2=CC=C(CN=NC3=NC=CC=C3Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.ar', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 14, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 9, 56, 56, 80, 80, 80, 80, 80, 80, 1, 12, 12, 12, 12, 1, 1, 9, 9, 80, 80, 80, 12] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34])
total number of confs: 140
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040170 none O=C([O-])C1=CC=CC(C2=CC=C(CN=NC3=NC=CC=C3Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.ar', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 14, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 67, 201, 201, 201, 201, 201, 201, 201, 201, 12, 1, 1, 1, 1, 12, 12, 67, 67, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 23, 24, 25, 26] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 399
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040170 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040170/1 /scratch/stefan/7769621/working/building/REAL300000040170 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 246)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/246
`/scratch/stefan/7769621/working/3D/246' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=NC=CC=C3Cl)S2)=C1)

`REAL300000040170.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040170.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040170/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040170 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=NC=CC=C3Cl)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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.ar', '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, 8, 1, 8, 1, 1, 1, 1, 16, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 101, 100, 101, 101, 52, 52, 10, 1, 1, 1, 1, 1, 1, 1, 1, 101, 201, 201, 201, 201, 101, 101, 52, 10, 1, 1, 1, 201] 201
rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 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: 310
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: REAL300000040170 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=NC=CC=C3Cl)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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.ar', '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, 8, 1, 8, 1, 1, 1, 1, 16, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 12, 13, 13, 1, 1, 1, 1, 1, 1, 9, 9, 45, 101, 101, 101, 101, 101, 101, 1, 13, 12, 13, 13, 1, 1, 9, 45, 101, 101, 101, 13] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34])
total number of confs: 201
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040170 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=NC=CC=C3Cl)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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.ar', '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, 8, 1, 8, 1, 1, 1, 1, 16, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 13, 13, 13, 13, 59, 59, 161, 201, 201, 201, 201, 201, 201, 13, 1, 1, 1, 1, 13, 13, 59, 161, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 23, 24, 25, 26] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 465
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040170 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040170
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040170/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040170/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040170
Building REAL300000040171
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040171'
/scratch/stefan/7769621/working/building/REAL300000040171 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040171

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040171/0 /scratch/stefan/7769621/working/building/REAL300000040171 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 247)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/247
`/scratch/stefan/7769621/working/3D/247' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC(C(=O)[O-])=C(C=NNC2=NC=CC=C2Cl)S1)

`REAL300000040171.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040171.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040171/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040171 none CCC1=CC(C(=O)[O-])=C(C=NNC2=NC=CC=C2Cl)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [72, 42, 42, 42, 41, 41, 43, 43, 31, 31, 9, 1, 1, 1, 1, 1, 1, 1, 1, 42, 72, 72, 72, 72, 72, 42, 31, 9, 1, 1, 1] 72
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 253
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040171 none CCC1=CC(C(=O)[O-])=C(C=NNC2=NC=CC=C2Cl)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 41, 41, 41, 41, 41, 41, 1, 9, 9, 9, 9, 9, 1, 3, 23, 41, 41, 41] 72
rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 19, 25] set([0, 6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30])
total number of confs: 111
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040171 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040171/1 /scratch/stefan/7769621/working/building/REAL300000040171 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 248)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/248
`/scratch/stefan/7769621/working/3D/248' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC(C(=O)[O-])=C(CN=NC2=NC=CC=C2Cl)S1)

`REAL300000040171.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040171.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040171/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040171 none CCC1=CC(C(=O)[O-])=C(CN=NC2=NC=CC=C2Cl)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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]
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, 68, 68, 68, 68, 68, 76, 76, 29, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 68, 135, 135, 135, 135, 135, 68, 28, 28, 1, 1, 1] 135
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 538
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040171 none CCC1=CC(C(=O)[O-])=C(CN=NC2=NC=CC=C2Cl)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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]
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: [7, 1, 1, 1, 1, 1, 3, 3, 1, 1, 5, 47, 47, 67, 67, 67, 67, 67, 68, 1, 7, 7, 7, 7, 7, 1, 5, 5, 68, 67, 68] 135
rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 19, 25] set([0, 6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30])
total number of confs: 129
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040171 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040171
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040171/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040171/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040171
Building REAL300000040172
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040172'
/scratch/stefan/7769621/working/building/REAL300000040172 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040172

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040172/0 /scratch/stefan/7769621/working/building/REAL300000040172 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 249)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/249
`/scratch/stefan/7769621/working/3D/249' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=NNC1=NC=CC=C1Cl)

`REAL300000040172.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040172.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040172/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040172 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=NC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
161  conformations in input
total number of sets (complete confs): 161
using faster count positions algorithm for large data
unique positions, atoms: [161, 160, 160, 160, 160, 160, 160, 160, 160, 160, 68, 67, 11, 1, 1, 1, 1, 1, 1, 1, 1, 161, 161, 161, 160, 160, 159, 67, 11, 1, 1, 1] 161
rigid atoms, others: [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])
total number of confs: 225
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040172 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=NC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
161  conformations in input
total number of sets (complete confs): 161
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 82, 159, 159, 159, 159, 159, 160, 4, 4, 4, 1, 1, 1, 12, 82, 159, 159, 159] 161
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31])
total number of confs: 312
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040172 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040172/1 /scratch/stefan/7769621/working/building/REAL300000040172 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 250)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/250
`/scratch/stefan/7769621/working/3D/250' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(=O)[O-])C=C1CN=NC1=NC=CC=C1Cl)

`REAL300000040172.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040172.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040172/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040172 none COC1=CC=C(C(=O)[O-])C=C1CN=NC1=NC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 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]
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, 115, 115, 115, 115, 115, 115, 115, 115, 115, 50, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 115, 115, 115, 50, 50, 1, 1, 1] 123
rigid atoms, others: [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])
total number of confs: 262
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040172 none COC1=CC=C(C(=O)[O-])C=C1CN=NC1=NC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 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]
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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 59, 60, 115, 115, 115, 115, 115, 115, 4, 4, 4, 1, 1, 1, 8, 8, 115, 115, 115] 123
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31])
total number of confs: 189
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040172 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040172
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040172/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040172/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040172
Building REAL300000040173
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040173'
/scratch/stefan/7769621/working/building/REAL300000040173 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040173

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040173/0 /scratch/stefan/7769621/working/building/REAL300000040173 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 251)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/251
`/scratch/stefan/7769621/working/3D/251' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2SC=C(C=NNC3=NC=CC=C3Cl)C2=C1)

`REAL300000040173.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040173.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040173/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040173 none O=C([O-])C1=CC=C2SC=C(C=NNC3=NC=CC=C3Cl)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 10, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 10, 1, 1, 1, 33] 33
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 53
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040173 none O=C([O-])C1=CC=C2SC=C(C=NNC3=NC=CC=C3Cl)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 6, 22, 33, 33, 33, 1] 33
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 30] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29])
total number of confs: 73
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040173 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040173
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040173/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040173
Building REAL300000040174
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040174'
/scratch/stefan/7769621/working/building/REAL300000040174 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040174

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040174/0 /scratch/stefan/7769621/working/building/REAL300000040174 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 252)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/252
`/scratch/stefan/7769621/working/3D/252' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2CCCC(N=NC3=NC=CC=C3Cl)C2=C1)

`REAL300000040174.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040174.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040174/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040174 none O=C([O-])C1=CN=C2CCCC(N=NC3=NC=CC=C3Cl)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.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']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 5, 5, 5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
8  conformations in input
total number of sets (complete confs): 8
using default count positions algorithm for smaller data
unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 8] 8
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 15
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040174 none O=C([O-])C1=CN=C2CCCC(N=NC3=NC=CC=C3Cl)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.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']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 5, 5, 5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 1] 8
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 32, 2, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31])
total number of confs: 13
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040174 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040174/1 /scratch/stefan/7769621/working/building/REAL300000040174 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 253)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/253
`/scratch/stefan/7769621/working/3D/253' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2CCCC(=NNC3=NC=CC=C3Cl)C2=C1)

`REAL300000040174.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040174.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040174/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040174 none O=C([O-])C1=CN=C2CCCC(=NNC3=NC=CC=C3Cl)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.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']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 17, 17, 17, 17, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 1, 1, 1, 17] 17
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 30
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040174 none O=C([O-])C1=CN=C2CCCC(=NNC3=NC=CC=C3Cl)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.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']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 1, 1, 7, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 1] 17
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 33, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 32, 2, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31])
total number of confs: 33
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040174 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040174
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040174/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040174/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040174
Building REAL300000040175
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040175'
/scratch/stefan/7769621/working/building/REAL300000040175 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040175

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040175/0 /scratch/stefan/7769621/working/building/REAL300000040175 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 254)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/254
`/scratch/stefan/7769621/working/3D/254' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(Br)C(C=NNC2=NC=CC=C2Cl)=C1)

`REAL300000040175.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040175.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040175/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040175 none O=C([O-])C1=CC=C(Br)C(C=NNC2=NC=CC=C2Cl)=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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [78, 78, 78, 78, 78, 78, 78, 78, 48, 48, 11, 1, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 48, 11, 1, 1, 1, 78] 78
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 27])
total number of confs: 120
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040175 none O=C([O-])C1=CC=C(Br)C(C=NNC2=NC=CC=C2Cl)=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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 12, 12, 47, 78, 78, 78, 78, 78, 78, 1, 1, 1, 12, 47, 78, 78, 78, 1] 78
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 27] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26])
total number of confs: 166
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040175 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040175
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040175/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040175
Building REAL300000040176
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040176'
/scratch/stefan/7769621/working/building/REAL300000040176 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040176

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040176/0 /scratch/stefan/7769621/working/building/REAL300000040176 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 255)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/255
`/scratch/stefan/7769621/working/3D/255' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(CN=NC2=NC=CC=C2Cl)=CC=C1C(=O)[O-])

`REAL300000040176.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040176.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040176/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040176 none COC1=CC(CN=NC2=NC=CC=C2Cl)=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.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']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 117, 117, 117, 27, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 173, 173, 201, 201, 201, 117, 27, 27, 1, 1, 1, 117, 117] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 585
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040176 none COC1=CC(CN=NC2=NC=CC=C2Cl)=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.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']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 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]
0  hydrogens 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, 66, 66, 116, 116, 116, 116, 116, 117, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 8, 8, 116, 116, 117, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 15, 16, 17, 18, 24, 30, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 25, 26, 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/7769621/working/building/REAL300000040176 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040176/1 /scratch/stefan/7769621/working/building/REAL300000040176 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 256)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/256
`/scratch/stefan/7769621/working/3D/256' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=NC=CC=C2Cl)=CC=C1C(=O)[O-])

`REAL300000040176.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040176.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040176/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040176 none COC1=CC(C=NNC2=NC=CC=C2Cl)=CC=C1C(=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', 'N.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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 154, 154, 154, 54, 54, 11, 1, 1, 1, 1, 1, 1, 1, 1, 154, 154, 154, 154, 201, 201, 201, 201, 201, 154, 54, 11, 1, 1, 1, 154, 154] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 499
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040176 none COC1=CC(C=NNC2=NC=CC=C2Cl)=CC=C1C(=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', 'N.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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 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
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, 13, 13, 58, 154, 154, 154, 154, 154, 154, 1, 1, 1, 1, 3, 3, 4, 4, 4, 1, 13, 58, 154, 154, 154, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 15, 16, 17, 18, 24, 30, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29])
total number of confs: 275
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040176 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040176
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040176/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040176/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040176
Building REAL300000040177
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040177'
/scratch/stefan/7769621/working/building/REAL300000040177 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040177

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040177/0 /scratch/stefan/7769621/working/building/REAL300000040177 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 257)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/257
`/scratch/stefan/7769621/working/3D/257' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(F)=C(C=NNC2=NC=CC=C2Cl)C(F)=C1)

`REAL300000040177.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040177.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040177/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040177 none O=C([O-])C1=CC(F)=C(C=NNC2=NC=CC=C2Cl)C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [42, 34, 42, 34, 42, 42, 42, 33, 33, 11, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 33, 11, 1, 1, 1, 42] 42
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 27])
total number of confs: 128
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040177 none O=C([O-])C1=CC(F)=C(C=NNC2=NC=CC=C2Cl)C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 27, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 7, 27, 41, 41, 41, 1] 42
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 27] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26])
total number of confs: 97
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040177 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040177
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040177/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040177
Building REAL300000040178
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040178'
/scratch/stefan/7769621/working/building/REAL300000040178 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040178

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040178/0 /scratch/stefan/7769621/working/building/REAL300000040178 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 258)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/258
`/scratch/stefan/7769621/working/3D/258' -> `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=NNC2=NC=CC=C2Cl)=C1)

`REAL300000040178.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040178.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040178/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040178 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=NC=CC=C2Cl)=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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [73, 73, 73, 73, 73, 73, 73, 73, 73, 46, 46, 11, 1, 1, 1, 1, 1, 1, 1, 1, 73, 73, 146, 46, 11, 1, 1, 1, 73] 146
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 28])
total number of confs: 261
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040178 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=NC=CC=C2Cl)=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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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, 1, 12, 12, 47, 73, 73, 73, 73, 73, 73, 1, 1, 2, 12, 47, 73, 73, 73, 1] 146
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27])
total number of confs: 157
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040178 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040178/1 /scratch/stefan/7769621/working/building/REAL300000040178 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 259)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/259
`/scratch/stefan/7769621/working/3D/259' -> `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=NNC2=NC=CC=C2Cl)=C1)

`REAL300000040178.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040178.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040178/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040178 none O=C([O-])C1=CC(Br)=C([O-])C(C=NNC2=NC=CC=C2Cl)=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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 30, 30, 29, 29, 9, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 29, 9, 1, 1, 1, 30] 30
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 27])
total number of confs: 48
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040178 none O=C([O-])C1=CC(Br)=C([O-])C(C=NNC2=NC=CC=C2Cl)=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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 30, 30, 30, 30, 30, 30, 1, 1, 6, 18, 30, 30, 30, 1] 30
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26])
total number of confs: 60
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040178 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040178
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040178/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040178/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040178
Building REAL300000040179
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040179'
/scratch/stefan/7769621/working/building/REAL300000040179 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040179

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040179/0 /scratch/stefan/7769621/working/building/REAL300000040179 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 260)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/260
`/scratch/stefan/7769621/working/3D/260' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(COC2=CC=C(CN=NC3=NC=CC=C3Cl)C=C2)O1)

`REAL300000040179.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040179.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040179/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040179 none O=C([O-])C1=CC=C(COC2=CC=C(CN=NC3=NC=CC=C3Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.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, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 12, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 94, 94, 73, 25, 94, 94, 24, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 94, 94, 201, 201, 201, 94, 94, 94, 94, 24, 24, 1, 1, 1, 94, 94] 201
rigid atoms, others: [34, 35, 36, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38])
total number of confs: 543
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: REAL300000040179 none O=C([O-])C1=CC=C(COC2=CC=C(CN=NC3=NC=CC=C3Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.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, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 12, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 8, 9, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 68, 68, 93, 93, 93, 93, 93, 94, 1, 1, 8, 8, 8, 1, 1, 1, 1, 8, 8, 93, 93, 94, 1, 1] 201
rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 32, 33, 34, 35, 36])
total number of confs: 155
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040179 none O=C([O-])C1=CC=C(COC2=CC=C(CN=NC3=NC=CC=C3Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.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, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 12, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 55, 196, 196, 201, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 8, 8, 8, 8, 55, 55, 201, 201, 201, 8, 8] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 398
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040179 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040179
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040179/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040179
Building REAL300000040180
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040180'
/scratch/stefan/7769621/working/building/REAL300000040180 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040180

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040180/0 /scratch/stefan/7769621/working/building/REAL300000040180 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 261)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/261
`/scratch/stefan/7769621/working/3D/261' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=NC=CC=C2Cl)=C1O)

`REAL300000040180.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040180.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040180/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040180 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=NC=CC=C2Cl)=C1O 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.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', '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, 8, 1, 8, 1, 1, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
172  conformations in input
total number of sets (complete confs): 172
using faster count positions algorithm for large data
unique positions, atoms: [86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 45, 45, 11, 1, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 86, 86, 86, 45, 11, 1, 1, 1, 172] 172
rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 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: 300
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040180 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=NC=CC=C2Cl)=C1O 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.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', '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, 8, 1, 8, 1, 1, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 48, 86, 86, 86, 86, 86, 86, 1, 1, 1, 1, 1, 1, 1, 11, 48, 86, 86, 86, 2] 172
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28] set([0, 32, 2, 34, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31])
total number of confs: 178
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040180 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040180
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040180/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040180
Building REAL300000040181
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040181'
/scratch/stefan/7769621/working/building/REAL300000040181 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040181

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040181/0 /scratch/stefan/7769621/working/building/REAL300000040181 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 262)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/262
`/scratch/stefan/7769621/working/3D/262' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CC1=CC=CC(C2=CC=C(CN=NC3=NC=CC=C3Cl)C=C2)=C1)

`REAL300000040181.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040181.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040181/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040181 none O=C([O-])CC1=CC=CC(C2=CC=C(CN=NC3=NC=CC=C3Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 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, 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, 142, 142, 89, 142, 142, 89, 54, 89, 89, 28, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 89, 89, 142, 201, 201, 89, 142, 142, 89, 89, 28, 28, 1, 1, 1, 89, 89, 142] 201
rigid atoms, others: [35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40])
total number of confs: 921
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: REAL300000040181 none O=C([O-])CC1=CC=CC(C2=CC=C(CN=NC3=NC=CC=C3Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 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, 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, 5, 11, 3, 3, 2, 3, 3, 1, 1, 1, 1, 1, 1, 8, 59, 59, 89, 89, 89, 89, 89, 89, 1, 1, 3, 5, 5, 2, 3, 3, 1, 1, 8, 8, 89, 89, 89, 1, 1, 3] 201
rigid atoms, others: [32, 38, 39, 8, 9, 10, 11, 12, 13, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 40])
total number of confs: 178
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040181 none O=C([O-])CC1=CC=CC(C2=CC=C(CN=NC3=NC=CC=C3Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 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, 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: [7, 3, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 17, 105, 105, 142, 142, 142, 142, 142, 142, 3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 17, 17, 142, 142, 142, 3, 3, 1] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 40, 25, 28, 29, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 250
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040181 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040181
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040181/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040181
Building REAL300000040182
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040182'
/scratch/stefan/7769621/working/building/REAL300000040182 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040182

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040182/0 /scratch/stefan/7769621/working/building/REAL300000040182 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 263)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/263
`/scratch/stefan/7769621/working/3D/263' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NNC2=NC=CC=C2Cl)SC(Cl)=C1)

`REAL300000040182.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040182.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040182/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040182 none O=C([O-])C1=C(C=NNC2=NC=CC=C2Cl)SC(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 14, 1, 16, 1, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [32, 31, 32, 31, 25, 25, 9, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 25, 9, 1, 1, 1, 32] 32
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 24])
total number of confs: 60
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040182 none O=C([O-])C1=C(C=NNC2=NC=CC=C2Cl)SC(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 14, 1, 16, 1, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 3, 3, 17, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 3, 17, 31, 31, 31, 1] 32
rigid atoms, others: [1, 3, 4, 5, 15, 16, 17, 18, 24] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23])
total number of confs: 68
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040182 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040182
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040182/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040182
Building REAL300000040183
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040183'
/scratch/stefan/7769621/working/building/REAL300000040183 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040183

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040183/0 /scratch/stefan/7769621/working/building/REAL300000040183 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 264)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/264
`/scratch/stefan/7769621/working/3D/264' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC(CN=NC2=NC=CC=C2Cl)=CC=C1OCC(=O)[O-])

`REAL300000040183.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040183.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040183/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040183 none CCOC1=CC(CN=NC2=NC=CC=C2Cl)=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.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 11, 11, 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, 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]
0  hydrogens 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, 86, 45, 45, 45, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 160, 199, 201, 201, 98, 98, 98, 98, 98, 45, 9, 9, 1, 1, 1, 45, 45, 199, 199] 201
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])
total number of confs: 613
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040183 none CCOC1=CC(CN=NC2=NC=CC=C2Cl)=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.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 11, 11, 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, 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]
0  hydrogens 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, 6, 44, 44, 44, 44, 44, 44, 44, 45, 1, 1, 1, 1, 7, 23, 35, 35, 5, 5, 5, 5, 5, 1, 6, 6, 44, 44, 45, 1, 1, 23, 23] 201
rigid atoms, others: [19, 2, 3, 4, 5, 6, 16, 17, 18, 35, 36, 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, 37, 38])
total number of confs: 197
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040183 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040183/1 /scratch/stefan/7769621/working/building/REAL300000040183 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 265)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/265
`/scratch/stefan/7769621/working/3D/265' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC(C=NNC2=NC=CC=C2Cl)=CC=C1OCC(=O)[O-])

`REAL300000040183.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040183.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040183/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040183 none CCOC1=CC(C=NNC2=NC=CC=C2Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 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]
0  hydrogens 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, 64, 29, 29, 29, 12, 11, 3, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 110, 190, 195, 195, 82, 82, 82, 82, 82, 29, 11, 3, 1, 1, 1, 29, 29, 190, 190] 201
rigid atoms, others: [32, 33, 34, 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, 35, 36, 37, 38])
total number of confs: 713
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040183 none CCOC1=CC(C=NNC2=NC=CC=C2Cl)=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 9, 1, 1, 1, 1, 1, 7, 7, 17, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 9, 38, 61, 61, 22, 22, 22, 22, 22, 1, 7, 17, 29, 29, 29, 1, 1, 38, 38] 201
rigid atoms, others: [19, 2, 3, 4, 5, 6, 16, 17, 18, 35, 36, 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, 37, 38])
total number of confs: 325
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040183 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040183
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040183/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040183/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040183
Building REAL300000040184
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040184'
/scratch/stefan/7769621/working/building/REAL300000040184 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040184

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040184/0 /scratch/stefan/7769621/working/building/REAL300000040184 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 266)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/266
`/scratch/stefan/7769621/working/3D/266' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC1=NC=CC=C1Cl)

`REAL300000040184.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040184.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040184/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040184 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC1=NC=CC=C1Cl 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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [47, 42, 47, 42, 42, 42, 42, 113, 113, 113, 113, 113, 42, 37, 37, 11, 1, 1, 1, 1, 1, 1, 1, 1, 113, 113, 113, 113, 113, 113, 113, 113, 113, 42, 37, 11, 1, 1, 1] 113
rigid atoms, others: [36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
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: REAL300000040184 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC1=NC=CC=C1Cl 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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [19, 13, 19, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 23, 23, 75, 113, 113, 113, 113, 113, 113, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 23, 75, 113, 113, 113] 113
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38])
total number of confs: 266
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040184 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC1=NC=CC=C1Cl 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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
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, 20, 42, 42, 42, 42, 42, 42, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 4, 20, 42, 42, 42] 113
rigid atoms, others: [1, 3, 4, 5, 6, 33, 12, 13, 14] set([0, 2, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 108
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040184 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040184
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040184/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040184
Building REAL300000040185
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040185'
/scratch/stefan/7769621/working/building/REAL300000040185 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040185

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040185/0 /scratch/stefan/7769621/working/building/REAL300000040185 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 267)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/267
`/scratch/stefan/7769621/working/3D/267' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C)C(C=NNC2=NC=CC=C2Cl)=C1C(=O)[O-])

`REAL300000040185.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040185.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040185/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040185 none COC1=CC=C(C)C(C=NNC2=NC=CC=C2Cl)=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.ar', 'N.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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 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, 4, 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
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [100, 78, 78, 78, 78, 78, 78, 58, 58, 11, 1, 1, 1, 1, 1, 1, 1, 1, 78, 78, 100, 100, 100, 100, 100, 78, 78, 78, 78, 78, 58, 11, 1, 1, 1] 100
rigid atoms, others: [32, 33, 34, 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])
total number of confs: 251
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040185 none COC1=CC=C(C)C(C=NNC2=NC=CC=C2Cl)=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.ar', 'N.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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 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, 4, 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
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 29, 78, 78, 78, 78, 78, 78, 1, 1, 3, 3, 4, 4, 4, 1, 1, 2, 2, 2, 6, 29, 78, 78, 78] 100
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])
total number of confs: 149
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040185 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040185/1 /scratch/stefan/7769621/working/building/REAL300000040185 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 268)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/268
`/scratch/stefan/7769621/working/3D/268' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C)C(CN=NC2=NC=CC=C2Cl)=C1C(=O)[O-])

`REAL300000040185.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040185.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040185/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040185 none COC1=CC=C(C)C(CN=NC2=NC=CC=C2Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'N.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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 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, 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
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [70, 65, 65, 65, 65, 65, 65, 44, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 70, 70, 70, 65, 65, 65, 65, 65, 44, 44, 1, 1, 1] 70
rigid atoms, others: [32, 33, 34, 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])
total number of confs: 183
number of broken/clashed sets: 53
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040185 none COC1=CC=C(C)C(CN=NC2=NC=CC=C2Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'N.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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 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, 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
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 33, 33, 65, 65, 65, 65, 65, 65, 1, 1, 2, 2, 4, 4, 4, 1, 1, 2, 2, 2, 5, 5, 65, 65, 65] 70
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])
total number of confs: 114
number of broken/clashed sets: 53
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040185 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040185
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040185/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040185/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040185
Building REAL300000040186
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040186'
/scratch/stefan/7769621/working/building/REAL300000040186 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040186

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040186/0 /scratch/stefan/7769621/working/building/REAL300000040186 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 269)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/269
`/scratch/stefan/7769621/working/3D/269' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C2=CC=C(F)C=C2C(CN=NC2=NC=CC=C2Cl)=C1C(=O)[O-])

`REAL300000040186.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040186.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040186/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040186 none CN1C2=CC=C(F)C=C2C(CN=NC2=NC=CC=C2Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 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, 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
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [66, 66, 66, 66, 66, 66, 66, 66, 66, 30, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 30, 30, 1, 1, 1] 66
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 154
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040186 none CN1C2=CC=C(F)C=C2C(CN=NC2=NC=CC=C2Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 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, 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
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 38, 38, 66, 66, 66, 66, 66, 66, 1, 1, 3, 3, 2, 2, 2, 1, 1, 1, 6, 6, 66, 66, 66] 66
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 27, 28, 29] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 118
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040186 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040186/1 /scratch/stefan/7769621/working/building/REAL300000040186 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 270)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/270
`/scratch/stefan/7769621/working/3D/270' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C2=CC=C(F)C=C2C(C=NNC2=NC=CC=C2Cl)=C1C(=O)[O-])

`REAL300000040186.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040186.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040186/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040186 none CN1C2=CC=C(F)C=C2C(C=NNC2=NC=CC=C2Cl)=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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 1, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 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, 4, 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
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 27, 25, 25, 9, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 25, 9, 1, 1, 1] 27
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 44
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040186 none CN1C2=CC=C(F)C=C2C(C=NNC2=NC=CC=C2Cl)=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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 1, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 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, 4, 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
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 18, 27, 27, 27, 27, 27, 27, 1, 1, 3, 3, 2, 2, 2, 1, 1, 1, 4, 18, 27, 27, 27] 27
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 27, 28, 29] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 69
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040186 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040186
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040186/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040186/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040186
Building REAL300000040187
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040187'
/scratch/stefan/7769621/working/building/REAL300000040187 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040187

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040187/0 /scratch/stefan/7769621/working/building/REAL300000040187 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 271)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/271
`/scratch/stefan/7769621/working/3D/271' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=NC=CC=C1Cl)C1=C(C(=O)[O-])C2=CC=CC=C2S1)

`REAL300000040187.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040187.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040187/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040187 none CC(N=NC1=NC=CC=C1Cl)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [6, 1, 6, 35, 35, 41, 41, 41, 41, 41, 41, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 41, 41, 41, 1, 1, 1, 1] 41
rigid atoms, others: [32, 1, 33, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040187 none CC(N=NC1=NC=CC=C1Cl)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 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, 2, 2, 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: [20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 20, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 20, 20, 20, 20, 1, 1, 1, 41, 41, 41, 41] 41
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 83
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040187 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040187
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040187/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040187
Building REAL300000040188
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040188'
/scratch/stefan/7769621/working/building/REAL300000040188 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040188

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040188/0 /scratch/stefan/7769621/working/building/REAL300000040188 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 272)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/272
`/scratch/stefan/7769621/working/3D/272' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NNC2=NC=CC=C2Cl)SC(Br)=C1)

`REAL300000040188.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040188.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040188/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040188 none O=C([O-])C1=C(C=NNC2=NC=CC=C2Cl)SC(Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 14, 1, 17, 1, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [32, 31, 32, 31, 25, 25, 9, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 25, 9, 1, 1, 1, 32] 32
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 24])
total number of confs: 60
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040188 none O=C([O-])C1=C(C=NNC2=NC=CC=C2Cl)SC(Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 14, 1, 17, 1, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 3, 3, 17, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 3, 17, 32, 31, 31, 1] 32
rigid atoms, others: [1, 3, 4, 5, 15, 16, 17, 18, 24] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23])
total number of confs: 70
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040188 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040188
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040188/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040188
Building REAL300000040189
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040189'
/scratch/stefan/7769621/working/building/REAL300000040189 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040189

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040189/0 /scratch/stefan/7769621/working/building/REAL300000040189 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 273)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/273
`/scratch/stefan/7769621/working/3D/273' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C2NC=C(CN=NC3=NC=CC=C3Cl)C2=CC=C1)

`REAL300000040189.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040189.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040189/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040189 none O=C([O-])C1=C2NC=C(CN=NC3=NC=CC=C3Cl)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [97, 97, 97, 97, 97, 97, 97, 33, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 97, 97, 97, 97, 97, 97, 33, 33, 1, 1, 1, 97, 97, 97] 97
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31])
total number of confs: 194
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040189 none O=C([O-])C1=C2NC=C(CN=NC3=NC=CC=C3Cl)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 9, 56, 57, 97, 97, 97, 97, 97, 97, 1, 1, 1, 1, 1, 1, 9, 9, 97, 97, 97, 1, 1, 1] 97
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 29, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28])
total number of confs: 162
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040189 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040189
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040189/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040189
Building REAL300000040190
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040190'
/scratch/stefan/7769621/working/building/REAL300000040190 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040190

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040190/0 /scratch/stefan/7769621/working/building/REAL300000040190 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 274)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/274
`/scratch/stefan/7769621/working/3D/274' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=NC=CC=C1Cl)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1)

`REAL300000040190.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040190.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040190/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040190 none CC(N=NC1=NC=CC=C1Cl)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 3, 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: [4, 1, 4, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 16, 16, 16, 1, 1, 1, 1, 1] 16
rigid atoms, others: [32, 1, 34, 35, 33, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 32
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040190 none CC(N=NC1=NC=CC=C1Cl)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 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, 2, 2, 7, 7, 7, 7, 7, 7, 3, 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, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 15, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 15, 15, 15, 15, 1, 1, 1, 16, 16, 16, 16, 16] 16
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35])
total number of confs: 46
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040190 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040190/1 /scratch/stefan/7769621/working/building/REAL300000040190 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 275)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/275
`/scratch/stefan/7769621/working/3D/275' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NC=CC=C1Cl)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1)

`REAL300000040190.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040190.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040190/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040190 none CC(=NNC1=NC=CC=C1Cl)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 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]
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, 15, 33, 33, 33, 33, 33, 33, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 15, 33, 33, 33, 1, 1, 1, 1, 1] 33
rigid atoms, others: [32, 1, 34, 35, 33, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 69
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040190 none CC(=NNC1=NC=CC=C1Cl)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 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]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [33, 33, 9, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 9, 1, 1, 1, 33, 33, 33, 33, 33] 33
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35])
total number of confs: 52
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040190 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040190
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040190/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040190/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040190
Building REAL300000040191
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040191'
/scratch/stefan/7769621/working/building/REAL300000040191 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040191

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040191/0 /scratch/stefan/7769621/working/building/REAL300000040191 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 276)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/276
`/scratch/stefan/7769621/working/3D/276' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC(CN=NC3=NC=CC=C3Cl)=CC=C2O1)

`REAL300000040191.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040191.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040191/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040191 none O=C([O-])C1=CC2=CC(CN=NC3=NC=CC=C3Cl)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [77, 77, 77, 77, 77, 77, 77, 35, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 77, 77, 77, 77, 77, 77, 34, 34, 1, 1, 1, 77, 77] 77
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30])
total number of confs: 172
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040191 none O=C([O-])C1=CC2=CC(CN=NC3=NC=CC=C3Cl)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 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, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 52, 52, 77, 77, 77, 77, 77, 77, 1, 1, 1, 1, 1, 1, 8, 8, 77, 77, 77, 1, 1] 77
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28])
total number of confs: 126
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040191 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040191/1 /scratch/stefan/7769621/working/building/REAL300000040191 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 277)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/277
`/scratch/stefan/7769621/working/3D/277' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC(C=NNC3=NC=CC=C3Cl)=CC=C2O1)

`REAL300000040191.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040191.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040191/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040191 none O=C([O-])C1=CC2=CC(C=NNC3=NC=CC=C3Cl)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 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, 63, 31, 31, 9, 1, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 63, 63, 31, 9, 1, 1, 1, 63, 63] 63
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30])
total number of confs: 107
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040191 none O=C([O-])C1=CC2=CC(C=NNC3=NC=CC=C3Cl)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 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, 1, 13, 13, 35, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 1, 13, 35, 63, 63, 63, 1, 1] 63
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28])
total number of confs: 135
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040191 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040191
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040191/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040191/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040191
Building REAL300000040192
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040192'
/scratch/stefan/7769621/working/building/REAL300000040192 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040192

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040192/0 /scratch/stefan/7769621/working/building/REAL300000040192 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 278)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/278
`/scratch/stefan/7769621/working/3D/278' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2C(C=NNC3=NC=CC=C3Cl)=CC=CN12)

`REAL300000040192.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040192.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040192/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040192 none O=C([O-])C1=CN=C2C(C=NNC3=NC=CC=C3Cl)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 9, 1, 1, 1, 27, 27, 27] 28
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30])
total number of confs: 44
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040192 none O=C([O-])C1=CN=C2C(C=NNC3=NC=CC=C3Cl)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 5, 17, 27, 27, 27, 1, 1, 1] 28
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27])
total number of confs: 56
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040192 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040192
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040192/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040192
Building REAL300000040193
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040193'
/scratch/stefan/7769621/working/building/REAL300000040193 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040193

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040193/0 /scratch/stefan/7769621/working/building/REAL300000040193 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 279)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/279
`/scratch/stefan/7769621/working/3D/279' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(COC2=CC=CC=C2CN=NC2=NC=CC=C2Cl)O1)

`REAL300000040193.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040193.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040193/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040193 none O=C([O-])C1=CC=C(COC2=CC=CC=C2CN=NC2=NC=CC=C2Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.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, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 12, 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, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [71, 71, 71, 71, 71, 71, 63, 51, 37, 37, 37, 27, 37, 37, 18, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 63, 63, 37, 37, 37, 37, 17, 17, 1, 1, 1] 71
rigid atoms, others: [36, 37, 38, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 230
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: REAL300000040193 none O=C([O-])C1=CC=C(COC2=CC=CC=C2CN=NC2=NC=CC=C2Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.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, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 12, 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, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [45, 45, 45, 45, 45, 45, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 31, 31, 37, 37, 37, 37, 37, 37, 45, 45, 45, 19, 19, 1, 1, 1, 1, 7, 7, 37, 37, 37] 71
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, 35, 36, 37, 38])
total number of confs: 157
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040193 none O=C([O-])C1=CC=C(COC2=CC=CC=C2CN=NC2=NC=CC=C2Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.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, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 12, 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, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 30, 45, 45, 31, 45, 45, 45, 55, 71, 71, 71, 71, 71, 71, 71, 71, 1, 1, 1, 7, 7, 45, 45, 45, 45, 55, 55, 71, 71, 71] 71
rigid atoms, others: [1, 3, 4, 5, 6, 7, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 224
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040193 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040193
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040193/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040193
Building REAL300000040194
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040194'
/scratch/stefan/7769621/working/building/REAL300000040194 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040194

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040194/0 /scratch/stefan/7769621/working/building/REAL300000040194 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 280)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/280
`/scratch/stefan/7769621/working/3D/280' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Br)C=CC=C1C=NNC1=NC=CC=C1Cl)

`REAL300000040194.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040194.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040194/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040194 none O=C([O-])C1=C(Br)C=CC=C1C=NNC1=NC=CC=C1Cl 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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 10, 1, 1, 1] 22
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24])
total number of confs: 38
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040194 none O=C([O-])C1=C(Br)C=CC=C1C=NNC1=NC=CC=C1Cl 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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 16, 22, 22, 22, 22, 22, 22, 1, 1, 1, 4, 16, 22, 22, 22] 22
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27])
total number of confs: 52
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040194 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040194
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040194/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040194
Building REAL300000040195
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040195'
/scratch/stefan/7769621/working/building/REAL300000040195 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040195

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040195/0 /scratch/stefan/7769621/working/building/REAL300000040195 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 281)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/281
`/scratch/stefan/7769621/working/3D/281' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2CN=NC1=NC=CC=C1Cl)

`REAL300000040195.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040195.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040195/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040195 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2CN=NC1=NC=CC=C1Cl 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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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
157  conformations in input
total number of sets (complete confs): 157
using faster count positions algorithm for large data
unique positions, atoms: [125, 83, 83, 83, 83, 83, 119, 83, 83, 83, 83, 83, 83, 117, 117, 40, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 125, 125, 125, 83, 119, 119, 119, 83, 83, 40, 40, 1, 1, 1] 157
rigid atoms, others: [37, 38, 39, 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])
total number of confs: 485
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040195 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2CN=NC1=NC=CC=C1Cl 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.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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
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, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 4, 36, 36, 82, 82, 82, 82, 82, 83, 2, 2, 2, 1, 3, 3, 3, 1, 1, 4, 4, 82, 82, 83] 157
rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 34, 15, 16, 33, 29] set([0, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 35, 36, 37, 38, 39])
total number of confs: 136
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040195 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040195/1 /scratch/stefan/7769621/working/building/REAL300000040195 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 282)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/282
`/scratch/stefan/7769621/working/3D/282' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NNC1=NC=CC=C1Cl)

`REAL300000040195.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040195.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040195/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040195 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NNC1=NC=CC=C1Cl 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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [113, 105, 105, 105, 105, 105, 107, 105, 105, 105, 105, 105, 105, 111, 111, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 113, 113, 113, 105, 107, 107, 107, 105, 105, 50, 11, 1, 1, 1] 113
rigid atoms, others: [37, 38, 39, 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])
total number of confs: 196
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040195 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NNC1=NC=CC=C1Cl 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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 8, 8, 46, 105, 105, 105, 105, 105, 105, 3, 3, 3, 1, 4, 4, 4, 1, 1, 8, 46, 105, 105, 105] 113
rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 34, 15, 16, 33, 29] set([0, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 35, 36, 37, 38, 39])
total number of confs: 212
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040195 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040195
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040195/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040195/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040195
Building REAL300000040196
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040196'
/scratch/stefan/7769621/working/building/REAL300000040196 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040196

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040196/0 /scratch/stefan/7769621/working/building/REAL300000040196 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 283)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/283
`/scratch/stefan/7769621/working/3D/283' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2OCOC2=C1C=NNC1=NC=CC=C1Cl)

`REAL300000040196.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040196.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040196/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040196 none O=C([O-])C1=CC=C2OCOC2=C1C=NNC1=NC=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 36, 36, 11, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 36, 11, 1, 1, 1] 51
rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27])
total number of confs: 85
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040196 none O=C([O-])C1=CC=C2OCOC2=C1C=NNC1=NC=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 3, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 29, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 6, 29, 51, 51, 51] 51
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25] set([0, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30])
total number of confs: 109
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040196 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040196/1 /scratch/stefan/7769621/working/building/REAL300000040196 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 284)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/284
`/scratch/stefan/7769621/working/3D/284' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2OCOC2=C1CN=NC1=NC=CC=C1Cl)

`REAL300000040196.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040196.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040196/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040196 none O=C([O-])C1=CC=C2OCOC2=C1CN=NC1=NC=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 26, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 26, 26, 1, 1, 1] 47
rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27])
total number of confs: 118
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040196 none O=C([O-])C1=CC=C2OCOC2=C1CN=NC1=NC=CC=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 38, 38, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 6, 6, 47, 47, 47] 47
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25] set([0, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30])
total number of confs: 79
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040196 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040196
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040196/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040196/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040196
Building REAL300000040197
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040197'
/scratch/stefan/7769621/working/building/REAL300000040197 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040197

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040197/0 /scratch/stefan/7769621/working/building/REAL300000040197 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 285)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/285
`/scratch/stefan/7769621/working/3D/285' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=CC=C(C(=O)[O-])C(C=NNC2=NC=CC=C2Cl)=C1)

`REAL300000040197.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040197.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040197/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040197 none N#CC1=CC=C(C(=O)[O-])C(C=NNC2=NC=CC=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 28, 23, 23, 10, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 23, 10, 1, 1, 1, 28] 28
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 28])
total number of confs: 48
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040197 none N#CC1=CC=C(C(=O)[O-])C(C=NNC2=NC=CC=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 4, 4, 19, 28, 28, 28, 28, 28, 28, 1, 1, 1, 4, 19, 28, 28, 28, 1] 28
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 20, 21, 22, 28] set([7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27])
total number of confs: 66
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040197 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040197
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040197/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040197
Building REAL300000040198
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040198'
/scratch/stefan/7769621/working/building/REAL300000040198 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040198

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040198/0 /scratch/stefan/7769621/working/building/REAL300000040198 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 286)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/286
`/scratch/stefan/7769621/working/3D/286' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(CN=NC2=NC=CC=C2Cl)C=C1Cl)

`REAL300000040198.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040198.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040198/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040198 none O=C([O-])COC1=CC=C(CN=NC2=NC=CC=C2Cl)C=C1Cl 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.3', 'N.2', 'N.2', 'C.ar', 'N.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: [11, 1, 11, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 16, 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, 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, 181, 63, 62, 63, 63, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 201, 201, 63, 63, 13, 13, 1, 1, 1, 63] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 398
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040198 none O=C([O-])COC1=CC=C(CN=NC2=NC=CC=C2Cl)C=C1Cl 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.3', 'N.2', 'N.2', 'C.ar', 'N.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: [11, 1, 11, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 16, 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, 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: [30, 21, 30, 7, 1, 1, 1, 1, 1, 1, 9, 59, 59, 63, 63, 63, 63, 63, 63, 1, 1, 1, 21, 21, 1, 1, 9, 9, 63, 63, 63, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 19, 20, 21, 24, 25, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27, 28, 29, 30])
total number of confs: 197
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040198 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040198/1 /scratch/stefan/7769621/working/building/REAL300000040198 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 287)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/287
`/scratch/stefan/7769621/working/3D/287' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC2=NC=CC=C2Cl)C=C1Cl)

`REAL300000040198.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040198.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040198/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040198 none O=C([O-])COC1=CC=C(C=NNC2=NC=CC=C2Cl)C=C1Cl 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', 'N.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: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 78, 46, 79, 78, 29, 29, 5, 1, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 201, 201, 79, 78, 29, 5, 1, 1, 1, 79] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 612
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040198 none O=C([O-])COC1=CC=C(C=NNC2=NC=CC=C2Cl)C=C1Cl 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', 'N.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: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [56, 33, 56, 7, 1, 1, 1, 1, 1, 1, 6, 6, 36, 78, 78, 78, 78, 78, 78, 1, 1, 1, 33, 33, 1, 1, 6, 36, 78, 78, 78, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 19, 20, 21, 24, 25, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27, 28, 29, 30])
total number of confs: 330
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040198 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040198
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040198/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040198/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040198
Building REAL300000040199
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040199'
/scratch/stefan/7769621/working/building/REAL300000040199 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040199

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040199/0 /scratch/stefan/7769621/working/building/REAL300000040199 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 288)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/288
`/scratch/stefan/7769621/working/3D/288' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CNS(=O)(=O)C1=CC=C(CN=NC2=NC=CC=C2Cl)C=C1)

`REAL300000040199.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040199.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040199/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040199 none O=C([O-])CNS(=O)(=O)C1=CC=C(CN=NC2=NC=CC=C2Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.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']
dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 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, 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, 185, 117, 48, 117, 117, 37, 117, 106, 23, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 117, 117, 201, 201, 185, 117, 117, 23, 23, 1, 1, 1, 117, 117] 201
rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35])
total number of confs: 1055
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040199 none O=C([O-])CNS(=O)(=O)C1=CC=C(CN=NC2=NC=CC=C2Cl)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.3', 'N.2', 'N.2', 'C.ar', 'N.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']
dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 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, 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, 9, 11, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 8, 66, 66, 116, 116, 116, 116, 116, 117, 1, 1, 9, 9, 5, 1, 1, 8, 8, 116, 116, 117, 1, 1] 201
rigid atoms, others: [34, 35, 5, 8, 9, 10, 11, 12, 22, 23, 27, 28] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33])
total number of confs: 239
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040199 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040199/1 /scratch/stefan/7769621/working/building/REAL300000040199 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 289)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/289
`/scratch/stefan/7769621/working/3D/289' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC2=NC=CC=C2Cl)C=C1)

`REAL300000040199.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040199.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040199/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040199 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC2=NC=CC=C2Cl)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', 'N.pl3', 'C.ar', 'N.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']
dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 57, 41, 18, 41, 41, 18, 41, 41, 18, 18, 4, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 65, 65, 57, 41, 41, 18, 4, 1, 1, 1, 41, 41] 65
rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35])
total number of confs: 343
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040199 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC2=NC=CC=C2Cl)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', 'N.pl3', 'C.ar', 'N.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']
dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 7, 7, 25, 41, 41, 41, 41, 41, 41, 1, 1, 9, 9, 5, 1, 1, 7, 25, 41, 41, 41, 1, 1] 65
rigid atoms, others: [34, 35, 5, 8, 9, 10, 11, 12, 22, 23, 27, 28] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33])
total number of confs: 127
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040199 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040199
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040199/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040199/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040199
Building REAL300000040200
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040200'
/scratch/stefan/7769621/working/building/REAL300000040200 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040200

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040200/0 /scratch/stefan/7769621/working/building/REAL300000040200 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 290)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/290
`/scratch/stefan/7769621/working/3D/290' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=C(C=NNC3=NC=CC=C3Cl)C(F)=CC=C2S1)

`REAL300000040200.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040200.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040200/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040200 none O=C([O-])C1=CC2=C(C=NNC3=NC=CC=C3Cl)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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [63, 62, 63, 62, 62, 63, 37, 37, 11, 1, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 63, 63, 62, 37, 11, 1, 1, 1, 63, 63] 63
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30])
total number of confs: 104
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040200 none O=C([O-])C1=CC2=C(C=NNC3=NC=CC=C3Cl)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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 11, 11, 39, 62, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 1, 1, 11, 39, 62, 62, 62, 1, 1] 63
rigid atoms, others: [1, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28])
total number of confs: 142
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040200 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040200
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040200/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040200
Building REAL300000040201
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040201'
/scratch/stefan/7769621/working/building/REAL300000040201 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040201

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040201/0 /scratch/stefan/7769621/working/building/REAL300000040201 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 291)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/291
`/scratch/stefan/7769621/working/3D/291' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(=O)[O-])=CC=C1CN=NC1=NC=CC=C1Cl)

`REAL300000040201.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040201.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040201/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040201 none COC1=CC(C(=O)[O-])=CC=C1CN=NC1=NC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 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]
0  hydrogens need rotated
130  conformations in input
total number of sets (complete confs): 130
using faster count positions algorithm for large data
unique positions, atoms: [130, 130, 130, 130, 130, 130, 130, 130, 130, 130, 57, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 130, 130, 130, 130, 130, 130, 56, 56, 1, 1, 1] 130
rigid atoms, others: [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])
total number of confs: 284
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040201 none COC1=CC(C(=O)[O-])=CC=C1CN=NC1=NC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 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]
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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 54, 54, 130, 130, 130, 130, 130, 130, 4, 4, 4, 1, 1, 1, 8, 8, 130, 130, 130] 130
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31])
total number of confs: 201
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040201 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040201/1 /scratch/stefan/7769621/working/building/REAL300000040201 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 292)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/292
`/scratch/stefan/7769621/working/3D/292' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=NNC1=NC=CC=C1Cl)

`REAL300000040201.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040201.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040201/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040201 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=NC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 39, 39, 11, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 52, 39, 11, 1, 1, 1] 52
rigid atoms, others: [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])
total number of confs: 82
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040201 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=NC=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 29, 52, 52, 52, 52, 52, 52, 4, 4, 4, 1, 1, 1, 8, 29, 52, 52, 52] 52
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31])
total number of confs: 115
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040201 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040201
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040201/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040201/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040201
Building REAL300000040202
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040202'
/scratch/stefan/7769621/working/building/REAL300000040202 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040202

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040202/0 /scratch/stefan/7769621/working/building/REAL300000040202 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 293)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/293
`/scratch/stefan/7769621/working/3D/293' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])[C@H]1C[C@H](N2C=CC(CN=NC3=NC=CC=C3Cl)=N2)C1)

`REAL300000040202.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040202.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040202/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040202 none O=C([O-])[C@H]1C[C@H](N2C=CC(CN=NC3=NC=CC=C3Cl)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 8, 5, 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, 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, 46, 201, 46, 46, 46, 12, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 46, 201, 201, 201, 46, 46, 12, 12, 1, 1, 1, 201, 201] 201
rigid atoms, others: [32, 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, 33, 34])
total number of confs: 473
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: REAL300000040202 none O=C([O-])[C@H]1C[C@H](N2C=CC(CN=NC3=NC=CC=C3Cl)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 8, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 11, 20, 11, 11, 11, 1, 11, 1, 1, 1, 1, 1, 6, 42, 42, 46, 46, 46, 46, 46, 46, 1, 11, 11, 11, 1, 1, 6, 6, 46, 46, 46, 11, 11] 201
rigid atoms, others: [6, 8, 9, 10, 11, 12, 22, 26, 27] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 126
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040202 none O=C([O-])[C@H]1C[C@H](N2C=CC(CN=NC3=NC=CC=C3Cl)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 5, 8, 8, 1, 8, 1, 1, 1, 1, 16, 8, 5, 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, 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, 3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 39, 197, 197, 201, 201, 201, 201, 201, 201, 11, 1, 1, 1, 11, 11, 39, 39, 201, 201, 201, 1, 1] 201
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 23, 24, 25, 33] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 330
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040202 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040202
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040202/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040202
Building REAL300000040203
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040203'
/scratch/stefan/7769621/working/building/REAL300000040203 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040203

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040203/0 /scratch/stefan/7769621/working/building/REAL300000040203 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 294)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/294
`/scratch/stefan/7769621/working/3D/294' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=CC=C2OCC(=O)[O-])C=C1)

`REAL300000040203.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040203.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040203/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040203 none COC1=CC=C(CNN=CC2=CC=CC=C2OCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 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]
0  hydrogens 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, 60, 35, 86, 86, 35, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 31, 57, 57, 86, 86, 86, 86, 86, 86, 86, 35, 35, 12, 4, 1, 1, 1, 1, 31, 31, 86, 86] 201
rigid atoms, others: [32, 33, 34, 35, 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, 36, 37, 38, 39])
total number of confs: 580
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040203 none COC1=CC=C(CNN=CC2=CC=CC=C2OCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations 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, 32, 62, 62, 86, 86, 63, 86, 86, 86, 151, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 6, 6, 32, 62, 86, 86, 86, 86, 201, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 38, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 640
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040203 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040203
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040203/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040203
Building REAL300000040204
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040204'
/scratch/stefan/7769621/working/building/REAL300000040204 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040204

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040204/0 /scratch/stefan/7769621/working/building/REAL300000040204 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 295)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/295
`/scratch/stefan/7769621/working/3D/295' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=C(OCC(=O)[O-])C=C2)C=C1)

`REAL300000040204.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040204.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040204/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040204 none COC1=CC=C(CNN=CC2=CC=C(OCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', '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, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 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]
0  hydrogens 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, 54, 68, 68, 34, 8, 4, 4, 1, 1, 1, 1, 1, 1, 6, 22, 39, 39, 1, 1, 68, 68, 68, 68, 68, 68, 68, 34, 34, 8, 4, 1, 1, 23, 23, 1, 1, 68, 68] 201
rigid atoms, others: [32, 33, 36, 37, 9, 10, 11, 12, 13, 14, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 38, 39])
total number of confs: 358
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040204 none COC1=CC=C(CNN=CC2=CC=C(OCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', '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, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations 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, 28, 52, 52, 68, 68, 52, 53, 153, 201, 201, 201, 68, 68, 1, 1, 2, 2, 2, 1, 1, 6, 6, 28, 52, 68, 68, 201, 201, 68, 68, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 38, 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])
total number of confs: 601
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040204 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040204
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040204/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040204
Building REAL300000040205
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040205'
/scratch/stefan/7769621/working/building/REAL300000040205 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040205

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040205/0 /scratch/stefan/7769621/working/building/REAL300000040205 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 296)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/296
`/scratch/stefan/7769621/working/3D/296' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC(Br)=CC=C2OCC(=O)[O-])C=C1)

`REAL300000040205.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040205.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040205/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040205 none COC1=CC=C(CNN=CC2=CC(Br)=CC=C2OCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 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, 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]
0  hydrogens 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, 83, 46, 84, 84, 40, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 33, 54, 54, 84, 84, 84, 84, 84, 84, 84, 40, 40, 13, 4, 1, 1, 1, 33, 33, 84, 84] 201
rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39])
total number of confs: 517
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040205 none COC1=CC=C(CNN=CC2=CC(Br)=CC=C2OCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations 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, 27, 54, 54, 84, 84, 84, 54, 84, 84, 84, 144, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 6, 6, 27, 54, 84, 84, 84, 201, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 38, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 674
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040205 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040205
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040205/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040205
Building REAL300000040206
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040206'
/scratch/stefan/7769621/working/building/REAL300000040206 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040206

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040206/0 /scratch/stefan/7769621/working/building/REAL300000040206 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 297)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/297
`/scratch/stefan/7769621/working/3D/297' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=CC(OC(C)C(=O)[O-])=C2)C=C1)

`REAL300000040206.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040206.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040206/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040206 none COC1=CC=C(CNN=CC2=CC=CC(OC(C)C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 7, 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, 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]
0  hydrogens 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, 63, 84, 84, 39, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 26, 26, 34, 34, 1, 84, 84, 85, 85, 85, 84, 84, 39, 39, 10, 4, 1, 1, 1, 26, 26, 26, 26, 1, 84, 84] 201
rigid atoms, others: [33, 34, 35, 40, 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, 32, 36, 37, 38, 39, 41, 42])
total number of confs: 416
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040206 none COC1=CC=C(CNN=CC2=CC=CC(OC(C)C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 7, 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, 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]
0  hydrogens need rotated
201  conformations 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, 31, 59, 59, 84, 84, 84, 84, 84, 171, 201, 201, 201, 201, 84, 1, 1, 2, 2, 2, 1, 1, 6, 6, 31, 59, 84, 84, 84, 201, 201, 201, 201, 84, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 42, 22, 23, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 469
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040206 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040206
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040206/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040206
Building REAL300000040207
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040207'
/scratch/stefan/7769621/working/building/REAL300000040207 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040207

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040207/0 /scratch/stefan/7769621/working/building/REAL300000040207 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 298)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/298
`/scratch/stefan/7769621/working/3D/298' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=CC(OCCC(=O)[O-])=C2)C=C1)

`REAL300000040207.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040207.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040207/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040207 none COC1=CC=C(CNN=CC2=CC=CC(OCCC(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 7, 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, 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]
0  hydrogens 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, 75, 37, 84, 84, 37, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 22, 22, 1, 84, 84, 85, 85, 85, 84, 84, 37, 37, 12, 6, 1, 1, 1, 15, 15, 15, 15, 1, 84, 84] 201
rigid atoms, others: [33, 34, 35, 40, 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, 32, 36, 37, 38, 39, 41, 42])
total number of confs: 467
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040207 none COC1=CC=C(CNN=CC2=CC=CC(OCCC(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 7, 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, 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]
0  hydrogens need rotated
201  conformations 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, 23, 49, 49, 84, 84, 84, 84, 84, 195, 201, 201, 201, 201, 84, 1, 1, 2, 2, 2, 1, 1, 6, 6, 23, 49, 84, 84, 84, 201, 201, 201, 201, 84, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 42, 22, 23, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 356
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040207 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040207
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040207/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040207
Building REAL300000040208
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040208'
/scratch/stefan/7769621/working/building/REAL300000040208 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040208

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040208/0 /scratch/stefan/7769621/working/building/REAL300000040208 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 299)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/299
`/scratch/stefan/7769621/working/3D/299' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)C=C1)

`REAL300000040208.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040208.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040208/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040208 none COC1=CC=C(CNN=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 162, 201, 201, 162, 79, 46, 46, 17, 17, 17, 17, 17, 10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 17, 201, 201, 201, 201, 201, 201, 201, 162, 162, 79, 46, 17, 16, 17, 6, 6, 1, 1, 1, 1, 17, 201, 201] 201
rigid atoms, others: [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, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49])
total number of confs: 851
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040208 none COC1=CC=C(CNN=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 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, 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]
0  hydrogens 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, 83, 50, 84, 84, 50, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 8, 17, 17, 16, 17, 17, 17, 20, 20, 1, 84, 84, 85, 85, 85, 84, 84, 50, 50, 14, 6, 1, 1, 1, 8, 8, 17, 17, 16, 17, 1, 84, 84] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 48, 49])
total number of confs: 460
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040208 none COC1=CC=C(CNN=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations 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, 20, 40, 40, 84, 84, 84, 84, 84, 116, 128, 201, 201, 200, 201, 201, 201, 201, 201, 84, 1, 1, 2, 2, 2, 1, 1, 6, 6, 20, 40, 84, 84, 84, 128, 128, 201, 201, 200, 201, 84, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 48, 49, 33, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 429
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040208 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040208
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040208/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040208
Building REAL300000040209
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040209'
/scratch/stefan/7769621/working/building/REAL300000040209 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040209

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040209/0 /scratch/stefan/7769621/working/building/REAL300000040209 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 300)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/300
`/scratch/stefan/7769621/working/3D/300' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)C=C1)

`REAL300000040209.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040209.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040209/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040209 none COC1=CC=C(CNN=CC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 1, 1, 1, 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, 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]
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: [93, 93, 55, 93, 93, 55, 14, 6, 6, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 1, 1, 2, 2, 1, 93, 93, 94, 94, 94, 93, 93, 55, 55, 14, 6, 1, 1, 5, 5, 1, 93, 93] 110
rigid atoms, others: [35, 36, 39, 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, 34, 37, 38, 40, 41])
total number of confs: 435
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040209 none COC1=CC=C(CNN=CC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 1, 1, 1, 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, 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]
0  hydrogens need rotated
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 24, 41, 41, 93, 93, 41, 69, 110, 110, 110, 110, 93, 93, 94, 94, 93, 1, 1, 2, 2, 2, 1, 1, 6, 6, 24, 41, 93, 93, 110, 110, 93, 1, 1] 110
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 40, 41, 24, 25, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 420
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040209 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040209
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040209/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040209
Building REAL300000040210
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040210'
/scratch/stefan/7769621/working/building/REAL300000040210 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040210

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040210/0 /scratch/stefan/7769621/working/building/REAL300000040210 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 301)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/301
`/scratch/stefan/7769621/working/3D/301' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=C(OCC3=CC(C)=C(C(=O)[O-])O3)C=C2)C=C1)

`REAL300000040210.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040210.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040210/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040210 none COC1=CC=C(CNN=CC2=CC=C(OCC3=CC(C)=C(C(=O)[O-])O3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 1, 1, 11, 11, 12, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 3, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 193, 201, 201, 143, 51, 31, 31, 16, 16, 16, 16, 9, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 16, 16, 201, 201, 201, 201, 201, 201, 201, 143, 143, 51, 31, 15, 16, 9, 9, 1, 2, 2, 2, 16, 16, 201, 201] 201
rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 707
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: REAL300000040210 none COC1=CC=C(CNN=CC2=CC=C(OCC3=CC(C)=C(C(=O)[O-])O3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 1, 1, 11, 11, 12, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 3, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [53, 53, 43, 53, 53, 28, 8, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 16, 16, 16, 16, 16, 28, 28, 16, 1, 1, 53, 53, 53, 53, 53, 53, 53, 28, 28, 8, 4, 1, 1, 3, 3, 16, 16, 16, 16, 1, 1, 53, 53] 201
rigid atoms, others: [38, 39, 9, 10, 11, 12, 13, 14, 47, 46, 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, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 48, 49])
total number of confs: 258
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040210 none COC1=CC=C(CNN=CC2=CC=C(OCC3=CC(C)=C(C(=O)[O-])O3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.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', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 1, 1, 11, 11, 12, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 3, 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
201  conformations 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, 22, 44, 44, 53, 53, 44, 45, 85, 85, 201, 201, 201, 201, 201, 201, 201, 201, 53, 53, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 44, 53, 53, 85, 85, 201, 201, 201, 201, 53, 53, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 48, 49, 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, 44, 45, 46, 47])
total number of confs: 380
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040210 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040210
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040210/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040210
Building REAL300000040211
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040211'
/scratch/stefan/7769621/working/building/REAL300000040211 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040211

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040211/0 /scratch/stefan/7769621/working/building/REAL300000040211 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 302)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/302
`/scratch/stefan/7769621/working/3D/302' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)C=C1)

`REAL300000040211.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040211.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040211/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040211 none COC1=CC=C(CNN=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 181, 201, 201, 181, 93, 56, 55, 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, 180, 180, 93, 56, 15, 16, 15, 8, 8, 1, 1, 1, 1, 15, 201, 201] 201
rigid atoms, others: [43, 44, 45, 46, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49])
total number of confs: 806
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: REAL300000040211 none COC1=CC=C(CNN=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [60, 59, 42, 60, 60, 42, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 15, 15, 15, 15, 16, 16, 16, 15, 1, 60, 60, 60, 61, 60, 60, 60, 42, 42, 12, 6, 1, 1, 1, 2, 2, 15, 15, 15, 15, 1, 60, 60] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 48, 49])
total number of confs: 287
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040211 none COC1=CC=C(CNN=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations 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, 22, 36, 36, 60, 60, 60, 60, 60, 89, 89, 200, 200, 200, 200, 200, 201, 201, 200, 60, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 36, 60, 60, 60, 89, 89, 200, 200, 200, 200, 60, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 48, 49, 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, 44, 45, 46, 47])
total number of confs: 348
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040211 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040211
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040211/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040211
Building REAL300000040212
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040212'
/scratch/stefan/7769621/working/building/REAL300000040212 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040212

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040212/0 /scratch/stefan/7769621/working/building/REAL300000040212 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 303)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/303
`/scratch/stefan/7769621/working/3D/303' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=CC(OCC(=O)[O-])=C2)C=C1)

`REAL300000040212.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040212.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040212/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040212 none COC1=CC=C(CNN=CC2=CC=CC(OCC(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', '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, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 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]
0  hydrogens 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, 61, 36, 73, 73, 36, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 23, 35, 35, 1, 73, 73, 73, 73, 73, 73, 73, 36, 36, 12, 5, 1, 1, 1, 23, 23, 1, 73, 73] 201
rigid atoms, others: [32, 33, 34, 37, 9, 10, 11, 12, 13, 14, 15, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 38, 39])
total number of confs: 449
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040212 none COC1=CC=C(CNN=CC2=CC=CC(OCC(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', '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, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations 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, 23, 49, 49, 73, 73, 73, 73, 73, 158, 201, 201, 201, 73, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 49, 73, 73, 73, 201, 201, 73, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 38, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 515
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040212 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040212
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040212/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040212
Building REAL300000040213
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040213'
/scratch/stefan/7769621/working/building/REAL300000040213 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040213

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040213/0 /scratch/stefan/7769621/working/building/REAL300000040213 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 304)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/304
`/scratch/stefan/7769621/working/3D/304' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=C(OC)C=C2OCC(=O)[O-])C=C1)

`REAL300000040213.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040213.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040213/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040213 none COC1=CC=C(CNN=CC2=CC=C(OC)C=C2OCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', '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, 1, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 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, 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]
0  hydrogens 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, 77, 50, 77, 77, 34, 10, 4, 4, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 7, 32, 50, 50, 77, 77, 77, 77, 77, 77, 77, 34, 34, 10, 4, 1, 1, 3, 3, 3, 1, 32, 32, 77, 77] 201
rigid atoms, others: [34, 35, 39, 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, 33, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 454
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040213 none COC1=CC=C(CNN=CC2=CC=C(OC)C=C2OCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', '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, 1, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 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, 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]
0  hydrogens need rotated
201  conformations 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, 30, 62, 62, 77, 77, 77, 77, 85, 77, 77, 77, 150, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 6, 6, 30, 62, 77, 77, 85, 85, 85, 77, 201, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 43, 23, 24, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 567
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040213 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040213
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040213/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040213
Building REAL300000040214
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040214'
/scratch/stefan/7769621/working/building/REAL300000040214 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040214

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040214/0 /scratch/stefan/7769621/working/building/REAL300000040214 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 305)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/305
`/scratch/stefan/7769621/working/3D/305' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)C=C1)

`REAL300000040214.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040214.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040214/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040214 none COC1=CC=C(CNN=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [36, 36, 27, 36, 36, 18, 8, 4, 4, 1, 1, 1, 1, 1, 1, 12, 45, 45, 44, 65, 65, 1, 1, 36, 36, 36, 36, 36, 36, 36, 18, 18, 8, 4, 1, 1, 1, 1, 36, 36] 201
rigid atoms, others: [34, 35, 36, 37, 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, 33, 38, 39])
total number of confs: 352
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040214 none COC1=CC=C(CNN=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations 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, 16, 28, 28, 36, 36, 28, 29, 120, 201, 201, 201, 201, 201, 36, 36, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 28, 36, 36, 36, 36, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 38, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 613
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040214 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040214
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040214/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040214
Building REAL300000040215
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040215'
/scratch/stefan/7769621/working/building/REAL300000040215 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040215

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040215/0 /scratch/stefan/7769621/working/building/REAL300000040215 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 306)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/306
`/scratch/stefan/7769621/working/3D/306' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=C(Br)C=C(C(=O)[O-])N2C)C=C1)

`REAL300000040215.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040215.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040215/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040215 none COC1=CC=C(CNN=CC2=C(Br)C=C(C(=O)[O-])N2C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', '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, 17, 1, 1, 1, 11, 11, 8, 5, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 150, 201, 201, 150, 64, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 150, 150, 64, 13, 1, 2, 2, 2, 201, 201] 201
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36])
total number of confs: 829
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040215 none COC1=CC=C(CNN=CC2=C(Br)C=C(C(=O)[O-])N2C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', '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, 17, 1, 1, 1, 11, 11, 8, 5, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations 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, 44, 147, 147, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 7, 7, 44, 147, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 35, 20, 21, 25, 26, 36] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 346
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040215 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040215
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040215/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040215
Building REAL300000040216
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040216'
/scratch/stefan/7769621/working/building/REAL300000040216 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040216

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040216/0 /scratch/stefan/7769621/working/building/REAL300000040216 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 307)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/307
`/scratch/stefan/7769621/working/3D/307' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=C(OCC(=O)[O-])C(Br)=C2)C=C1)

`REAL300000040216.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040216.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040216/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040216 none COC1=CC=C(CNN=CC2=CC=C(OCC(=O)[O-])C(Br)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 1, 1, 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, 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]
0  hydrogens 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, 42, 90, 90, 42, 15, 7, 7, 1, 1, 1, 1, 1, 1, 7, 32, 40, 40, 1, 1, 1, 90, 90, 90, 90, 90, 90, 90, 42, 42, 15, 7, 1, 1, 32, 32, 1, 90, 90] 201
rigid atoms, others: [33, 34, 37, 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, 32, 35, 36, 38, 39])
total number of confs: 544
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040216 none COC1=CC=C(CNN=CC2=CC=C(OCC(=O)[O-])C(Br)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations 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, 22, 43, 43, 90, 90, 68, 89, 175, 201, 201, 201, 90, 90, 90, 1, 1, 2, 2, 2, 1, 1, 6, 6, 22, 43, 90, 90, 201, 201, 90, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 38, 22, 23, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 562
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040216 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040216
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040216/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040216
Building REAL300000040217
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040217'
/scratch/stefan/7769621/working/building/REAL300000040217 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040217

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040217/0 /scratch/stefan/7769621/working/building/REAL300000040217 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 308)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/308
`/scratch/stefan/7769621/working/3D/308' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=C3C=C(C(=O)[O-])OC3=C(OC)C=C2)C=C1)

`REAL300000040217.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040217.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040217/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040217 none COC1=CC=C(CNN=CC2=C3C=C(C(=O)[O-])OC3=C(OC)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', '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, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 12, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 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]
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, 141, 98, 151, 151, 98, 36, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 151, 151, 151, 151, 151, 151, 151, 98, 98, 36, 12, 1, 3, 3, 3, 1, 1, 151, 151] 151
rigid atoms, others: [35, 39, 40, 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, 34, 36, 37, 38, 41, 42])
total number of confs: 647
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040217 none COC1=CC=C(CNN=CC2=C3C=C(C(=O)[O-])OC3=C(OC)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', '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, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 12, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 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]
0  hydrogens need rotated
151  conformations in input
total number of sets (complete confs): 151
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 36, 93, 93, 151, 151, 151, 151, 151, 151, 151, 151, 151, 151, 151, 151, 151, 1, 1, 2, 2, 2, 1, 1, 6, 6, 36, 93, 151, 151, 151, 151, 151, 151, 1, 1] 151
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 42, 24, 25, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 274
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040217 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040217
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040217/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040217
Building REAL300000040218
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040218'
/scratch/stefan/7769621/working/building/REAL300000040218 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040218

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040218/0 /scratch/stefan/7769621/working/building/REAL300000040218 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 309)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/309
`/scratch/stefan/7769621/working/3D/309' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=C3C=CC(C(=O)[O-])=CC3=NN2)C=C1)

`REAL300000040218.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040218.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040218/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040218 none COC1=CC=C(CNN=CC2=C3C=CC(C(=O)[O-])=CC3=NN2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 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]
0  hydrogens need rotated
151  conformations in input
total number of sets (complete confs): 151
using faster count positions algorithm for large data
unique positions, atoms: [151, 151, 115, 151, 151, 115, 37, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 151, 151, 151, 151, 151, 151, 151, 115, 115, 36, 7, 1, 1, 1, 1, 151, 151] 151
rigid atoms, others: [33, 34, 35, 36, 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, 32, 37, 38])
total number of confs: 610
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040218 none COC1=CC=C(CNN=CC2=C3C=CC(C(=O)[O-])=CC3=NN2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 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]
0  hydrogens need rotated
151  conformations in input
total number of sets (complete confs): 151
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 39, 127, 127, 151, 151, 151, 151, 151, 151, 151, 151, 151, 151, 151, 1, 1, 2, 2, 2, 1, 1, 6, 6, 39, 127, 151, 151, 151, 151, 1, 1] 151
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 38, 22, 23, 27, 28, 37] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 270
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040218 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040218/1 /scratch/stefan/7769621/working/building/REAL300000040218 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 310)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/310
`/scratch/stefan/7769621/working/3D/310' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=NNC3=CC(C(=O)[O-])=CC=C23)C=C1)

`REAL300000040218.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040218.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040218/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040218 none COC1=CC=C(CNN=CC2=NNC3=CC(C(=O)[O-])=CC=C23)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 152, 201, 201, 150, 60, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 150, 150, 60, 11, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [33, 34, 35, 36, 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, 32, 37, 38])
total number of confs: 807
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040218 none COC1=CC=C(CNN=CC2=NNC3=CC(C(=O)[O-])=CC=C23)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 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]
0  hydrogens need rotated
201  conformations 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, 43, 126, 126, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 7, 7, 43, 126, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 38, 22, 23, 27, 28, 37] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 363
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040218 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040218
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040218/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040218/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040218
Building REAL300000040219
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040219'
/scratch/stefan/7769621/working/building/REAL300000040219 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040219

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040219/0 /scratch/stefan/7769621/working/building/REAL300000040219 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 311)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/311
`/scratch/stefan/7769621/working/3D/311' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC(OC)=C(OCC(=O)[O-])C=C2[N+](=O)[O-])C=C1)

`REAL300000040219.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040219.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040219/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040219 none COC1=CC=C(CNN=CC2=CC(OC)=C(OCC(=O)[O-])C=C2[N+](=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 11, 11, 1, 1, 8, 11, 11, 1, 1, 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, 4, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [81, 81, 66, 81, 81, 44, 15, 7, 7, 1, 1, 1, 1, 1, 3, 1, 1, 9, 17, 23, 23, 1, 1, 1, 2, 2, 81, 81, 81, 81, 81, 81, 81, 44, 44, 15, 7, 1, 4, 4, 4, 17, 17, 1, 81, 81] 201
rigid atoms, others: [43, 37, 9, 10, 11, 12, 13, 15, 16, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 44, 45])
total number of confs: 363
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040219 none COC1=CC=C(CNN=CC2=CC(OC)=C(OCC(=O)[O-])C=C2[N+](=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 11, 11, 1, 1, 8, 11, 11, 1, 1, 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, 4, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 23, 45, 45, 81, 81, 81, 124, 81, 81, 193, 201, 201, 201, 81, 81, 81, 81, 81, 1, 1, 2, 2, 2, 1, 1, 6, 6, 23, 45, 81, 124, 124, 124, 201, 201, 81, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 44, 45, 26, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 459
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040219 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040219
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040219/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040219
Building REAL300000040220
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040220'
/scratch/stefan/7769621/working/building/REAL300000040220 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040220

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040220/0 /scratch/stefan/7769621/working/building/REAL300000040220 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 312)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/312
`/scratch/stefan/7769621/working/3D/312' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC(C(F)(F)F)=CC=C2N(C)CC(=O)[O-])C=C1)

`REAL300000040220.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040220.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040220/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040220 none COC1=CC=C(CNN=CC2=CC(C(F)(F)F)=CC=C2N(C)CC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 1, 11, 11, 1, 1, 7, 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, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [165, 164, 69, 165, 165, 69, 17, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 4, 4, 15, 23, 23, 165, 165, 165, 165, 165, 165, 165, 69, 69, 17, 4, 1, 1, 1, 4, 4, 4, 15, 15, 165, 165] 201
rigid atoms, others: [37, 38, 39, 9, 10, 11, 12, 13, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 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: 783
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040220 none COC1=CC=C(CNN=CC2=CC(C(F)(F)F)=CC=C2N(C)CC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 1, 11, 11, 1, 1, 7, 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, 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
201  conformations 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, 45, 129, 129, 165, 165, 165, 165, 165, 165, 149, 165, 165, 165, 177, 177, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 7, 7, 45, 129, 165, 165, 165, 177, 177, 177, 201, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 45, 46, 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, 25, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 548
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040220 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040220
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040220/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040220
Building REAL300000040221
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040221'
/scratch/stefan/7769621/working/building/REAL300000040221 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040221

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040221/0 /scratch/stefan/7769621/working/building/REAL300000040221 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 313)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/313
`/scratch/stefan/7769621/working/3D/313' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=C(OCCC(=O)[O-])C(OC)=C2)C=C1)

`REAL300000040221.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040221.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040221/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040221 none COC1=CC=C(CNN=CC2=CC=C(OCCC(=O)[O-])C(OC)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', '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, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 12, 5, 1, 1, 1, 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, 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]
0  hydrogens 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, 40, 78, 78, 40, 15, 7, 7, 1, 1, 1, 1, 1, 1, 9, 21, 21, 40, 38, 1, 1, 3, 1, 78, 78, 78, 78, 78, 78, 78, 40, 40, 15, 7, 1, 1, 21, 21, 21, 21, 3, 3, 3, 1, 78, 78] 201
rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 44, 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, 34, 37, 38, 39, 40, 41, 42, 43, 45, 46])
total number of confs: 490
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040221 none COC1=CC=C(CNN=CC2=CC=C(OCCC(=O)[O-])C(OC)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', '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, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 12, 5, 1, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations 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, 18, 33, 33, 78, 78, 77, 77, 164, 192, 192, 201, 197, 78, 78, 111, 78, 1, 1, 2, 2, 2, 1, 1, 6, 6, 18, 33, 78, 78, 192, 192, 192, 192, 111, 111, 111, 78, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 45, 46, 24, 25, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 537
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040221 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040221
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040221/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040221
Building REAL300000040222
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040222'
/scratch/stefan/7769621/working/building/REAL300000040222 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040222

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040222/0 /scratch/stefan/7769621/working/building/REAL300000040222 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 314)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/314
`/scratch/stefan/7769621/working/3D/314' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=C(C(=O)[O-])C=C2Cl)C=C1)

`REAL300000040222.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040222.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040222/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040222 none COC1=CC=C(CNN=CC2=CC=C(C(=O)[O-])C=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', '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, 1, 11, 11, 1, 1, 16, 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, 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]
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, 123, 165, 165, 123, 49, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 165, 165, 165, 165, 165, 165, 165, 123, 123, 49, 11, 1, 1, 1, 165, 165] 165
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])
total number of confs: 685
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040222 none COC1=CC=C(CNN=CC2=CC=C(C(=O)[O-])C=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', '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, 1, 11, 11, 1, 1, 16, 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, 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]
0  hydrogens need rotated
165  conformations in input
total number of sets (complete confs): 165
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 44, 143, 143, 165, 165, 153, 165, 165, 165, 165, 165, 165, 1, 1, 1, 1, 1, 1, 1, 6, 6, 44, 143, 165, 165, 165, 1, 1] 165
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 35, 20, 21, 22, 23, 24, 25, 26] set([32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31])
total number of confs: 342
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040222 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040222
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040222/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040222
Building REAL300000040223
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040223'
/scratch/stefan/7769621/working/building/REAL300000040223 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040223

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040223/0 /scratch/stefan/7769621/working/building/REAL300000040223 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 315)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/315
`/scratch/stefan/7769621/working/3D/315' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=C(O)C(C(=O)[O-])=C2)C=C1)

`REAL300000040223.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040223.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040223/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040223 none COC1=CC=C(CNN=CC2=CC=C(O)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', '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, 12, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 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]
1  hydrogens need rotated
226  conformations in input
total number of sets (complete confs): 226
using faster count positions algorithm for large data
unique positions, atoms: [113, 113, 109, 113, 113, 91, 32, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 113, 113, 113, 113, 113, 113, 113, 91, 91, 32, 8, 1, 1, 2, 1, 113, 113] 226
rigid atoms, others: [32, 34, 9, 10, 11, 12, 13, 14, 15, 16, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 35, 36])
total number of confs: 392
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040223 none COC1=CC=C(CNN=CC2=CC=C(O)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', '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, 12, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 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]
1  hydrogens need rotated
226  conformations in input
total number of sets (complete confs): 226
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 37, 83, 83, 113, 113, 113, 113, 113, 113, 113, 113, 113, 1, 1, 1, 1, 1, 1, 1, 6, 6, 37, 83, 113, 113, 226, 113, 1, 1] 226
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 35, 20, 21, 22, 23, 24, 25, 26, 36] set([32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31])
total number of confs: 451
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040223 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040223
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040223/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040223
Building REAL300000040224
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040224'
/scratch/stefan/7769621/working/building/REAL300000040224 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040224

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040224/0 /scratch/stefan/7769621/working/building/REAL300000040224 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 316)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/316
`/scratch/stefan/7769621/working/3D/316' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=C(OC(C)C(=O)[O-])C=C2)C=C1)

`REAL300000040224.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040224.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040224/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040224 none COC1=CC=C(CNN=CC2=CC=C(OC(C)C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', '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, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 7, 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, 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]
0  hydrogens 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, 80, 59, 81, 81, 35, 12, 4, 4, 1, 1, 1, 1, 1, 1, 11, 27, 27, 38, 38, 1, 1, 81, 81, 81, 81, 81, 81, 81, 35, 35, 12, 4, 1, 1, 27, 27, 27, 27, 1, 1, 81, 81] 201
rigid atoms, others: [33, 34, 39, 40, 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, 32, 35, 36, 37, 38, 41, 42])
total number of confs: 401
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040224 none COC1=CC=C(CNN=CC2=CC=C(OC(C)C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', '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, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 7, 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, 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]
0  hydrogens need rotated
201  conformations 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, 31, 61, 61, 81, 81, 61, 62, 171, 201, 201, 201, 201, 81, 81, 1, 1, 1, 1, 1, 1, 1, 6, 6, 31, 61, 81, 81, 201, 201, 201, 201, 81, 81, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 42, 22, 23, 24, 25, 26, 27, 28] set([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])
total number of confs: 537
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040224 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040224
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040224/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040224
Building REAL300000040225
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040225'
/scratch/stefan/7769621/working/building/REAL300000040225 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040225

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040225/0 /scratch/stefan/7769621/working/building/REAL300000040225 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 317)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/317
`/scratch/stefan/7769621/working/3D/317' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CN(CC(=O)[O-])C3=CC=CC=C23)C=C1)

`REAL300000040225.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040225.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040225/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040225 none COC1=CC=C(CNN=CC2=CN(CC(=O)[O-])C3=CC=CC=C23)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 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, 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]
0  hydrogens 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, 134, 85, 136, 136, 72, 20, 6, 6, 1, 1, 1, 1, 1, 8, 16, 16, 1, 1, 1, 1, 1, 1, 136, 136, 136, 137, 137, 137, 137, 73, 73, 20, 6, 1, 8, 8, 1, 1, 1, 1, 137, 137] 201
rigid atoms, others: [34, 37, 38, 39, 40, 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, 33, 35, 36, 41, 42])
total number of confs: 597
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040225 none COC1=CC=C(CNN=CC2=CN(CC(=O)[O-])C3=CC=CC=C23)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations 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, 34, 75, 75, 136, 136, 136, 201, 201, 201, 136, 136, 137, 137, 136, 136, 1, 1, 1, 1, 1, 1, 1, 6, 6, 34, 75, 136, 201, 201, 136, 137, 137, 137, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 42, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 595
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040225 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040225
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040225/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040225
Building REAL300000040226
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040226'
/scratch/stefan/7769621/working/building/REAL300000040226 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040226

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040226/0 /scratch/stefan/7769621/working/building/REAL300000040226 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 318)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/318
`/scratch/stefan/7769621/working/3D/318' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=C(C)C2=CC=CC(OCCCC(=O)[O-])=C2)C=C1)

`REAL300000040226.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040226.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040226/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040226 none COC1=CC=C(CNN=C(C)C2=CC=CC(OCCCC(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 1, 1, 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, 3, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [76, 68, 41, 76, 76, 41, 15, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 7, 14, 15, 25, 42, 42, 1, 76, 76, 76, 76, 76, 76, 76, 41, 41, 15, 9, 9, 9, 1, 1, 1, 15, 15, 14, 14, 25, 25, 1, 76, 76] 201
rigid atoms, others: [37, 38, 39, 9, 11, 12, 13, 14, 15, 16, 46, 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, 36, 40, 41, 42, 43, 44, 45, 47, 48])
total number of confs: 542
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040226 none COC1=CC=C(CNN=C(C)C2=CC=CC(OCCCC(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 1, 1, 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, 3, 7, 7, 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]
0  hydrogens need rotated
201  conformations 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, 15, 29, 29, 29, 76, 76, 76, 76, 76, 157, 182, 182, 201, 201, 201, 76, 1, 1, 2, 2, 2, 1, 1, 6, 6, 15, 30, 30, 30, 76, 76, 76, 182, 182, 182, 182, 201, 201, 76, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 47, 48, 24, 25, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 520
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040226 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040226
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040226/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040226
Building REAL300000040227
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040227'
/scratch/stefan/7769621/working/building/REAL300000040227 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040227

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040227/0 /scratch/stefan/7769621/working/building/REAL300000040227 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 319)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/319
`/scratch/stefan/7769621/working/3D/319' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=C(C)CCC2=CC=C(OC(C)C(=O)[O-])C=C2)C=C1)

`REAL300000040227.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040227.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040227/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040227 none COC1=CC=C(CNN=C(C)CCC2=CC=C(OC(C)C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.3', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 83, 55, 88, 88, 55, 22, 14, 14, 4, 14, 2, 1, 1, 1, 1, 1, 1, 9, 20, 20, 24, 24, 1, 1, 88, 88, 88, 88, 88, 88, 88, 55, 55, 22, 14, 14, 14, 4, 4, 2, 2, 1, 1, 20, 20, 20, 20, 1, 1, 88, 88] 201
rigid atoms, others: [48, 49, 42, 43, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 50, 51])
total number of confs: 493
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040227 none COC1=CC=C(CNN=C(C)CCC2=CC=C(OC(C)C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.3', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 14, 30, 30, 30, 76, 88, 88, 88, 88, 88, 187, 201, 201, 201, 201, 88, 88, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 31, 31, 31, 76, 76, 88, 88, 88, 88, 201, 201, 201, 201, 88, 88, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 50, 51, 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, 44, 45, 46, 47, 48, 49])
total number of confs: 551
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040227 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040227
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040227/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040227
Building REAL300000040228
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040228'
/scratch/stefan/7769621/working/building/REAL300000040228 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040228

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040228/0 /scratch/stefan/7769621/working/building/REAL300000040228 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 320)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/320
`/scratch/stefan/7769621/working/3D/320' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=C(C)CCC2=CC=C(OCC(=O)[O-])C=C2)C=C1)

`REAL300000040228.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040228.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040228/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040228 none COC1=CC=C(CNN=C(C)CCC2=CC=C(OCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 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, 3, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [92, 85, 57, 92, 92, 57, 24, 14, 14, 4, 14, 2, 1, 1, 1, 1, 1, 1, 6, 16, 30, 30, 1, 1, 92, 92, 92, 92, 92, 92, 92, 57, 57, 24, 14, 14, 14, 4, 4, 2, 2, 1, 1, 16, 16, 1, 1, 92, 92] 201
rigid atoms, others: [45, 41, 42, 12, 13, 14, 15, 16, 17, 46, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 47, 48])
total number of confs: 530
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040228 none COC1=CC=C(CNN=C(C)CCC2=CC=C(OCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 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, 3, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 14, 27, 27, 27, 80, 92, 92, 92, 92, 92, 179, 201, 201, 201, 92, 92, 1, 1, 2, 2, 2, 1, 1, 6, 6, 14, 28, 28, 28, 80, 80, 92, 92, 92, 92, 201, 201, 92, 92, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 47, 48, 24, 25, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 606
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040228 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040228
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040228/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040228
Building REAL300000040229
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040229'
/scratch/stefan/7769621/working/building/REAL300000040229 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040229

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040229/0 /scratch/stefan/7769621/working/building/REAL300000040229 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 321)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/321
`/scratch/stefan/7769621/working/3D/321' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=C(C)C2=CC=CC(OC(C)C(=O)[O-])=C2)C=C1)

`REAL300000040229.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040229.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040229/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040229 none COC1=CC=C(CNN=C(C)C2=CC=CC(OC(C)C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [92, 91, 73, 92, 92, 46, 16, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 11, 22, 22, 30, 30, 1, 92, 92, 92, 92, 92, 92, 92, 46, 46, 16, 8, 8, 8, 1, 1, 1, 22, 22, 22, 22, 1, 92, 92] 201
rigid atoms, others: [43, 36, 37, 38, 9, 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, 35, 39, 40, 41, 42, 44, 45])
total number of confs: 420
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040229 none COC1=CC=C(CNN=C(C)C2=CC=CC(OC(C)C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations 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, 20, 41, 41, 41, 92, 92, 92, 92, 92, 185, 201, 201, 201, 201, 92, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 42, 42, 42, 92, 92, 92, 201, 201, 201, 201, 92, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 44, 45, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 409
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040229 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040229
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040229/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040229
Building REAL300000040230
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040230'
/scratch/stefan/7769621/working/building/REAL300000040230 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040230

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040230/0 /scratch/stefan/7769621/working/building/REAL300000040230 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 322)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/322
`/scratch/stefan/7769621/working/3D/322' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=C(C)CCC2=CC=C(OCCC(=O)[O-])C=C2)C=C1)

`REAL300000040230.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040230.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040230/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040230 none COC1=CC=C(CNN=C(C)CCC2=CC=C(OCCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.3', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 79, 55, 84, 84, 55, 24, 12, 12, 3, 12, 1, 1, 1, 1, 1, 1, 1, 6, 8, 8, 15, 15, 1, 1, 84, 84, 84, 84, 84, 84, 84, 55, 55, 24, 12, 12, 12, 3, 3, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 84, 84] 201
rigid atoms, others: [48, 43, 49, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 50, 51])
total number of confs: 458
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040230 none COC1=CC=C(CNN=C(C)CCC2=CC=C(OCCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.3', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 11, 25, 25, 25, 78, 84, 84, 84, 84, 84, 201, 201, 201, 201, 199, 84, 84, 1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 26, 26, 26, 78, 78, 84, 84, 84, 84, 201, 201, 201, 201, 84, 84, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 50, 51, 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, 44, 45, 46, 47, 48, 49])
total number of confs: 483
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040230 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040230
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040230/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040230
Building REAL300000040231
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040231'
/scratch/stefan/7769621/working/building/REAL300000040231 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040231

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040231/0 /scratch/stefan/7769621/working/building/REAL300000040231 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 323)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/323
`/scratch/stefan/7769621/working/3D/323' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNCC1=CC=C(OC)C=C1)C1=CC=C(OCCCCC(=O)[O-])C=C1)

`REAL300000040231.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040231.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040231/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040231 none CCC(=NNCC1=CC=C(OC)C=C1)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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 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]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 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: [9, 6, 1, 6, 6, 14, 34, 34, 34, 34, 34, 54, 34, 34, 1, 1, 1, 1, 1, 6, 10, 19, 19, 21, 23, 27, 1, 1, 9, 9, 9, 9, 9, 14, 34, 34, 34, 34, 54, 54, 54, 34, 34, 1, 1, 10, 10, 18, 18, 19, 19, 20, 20, 1, 1] 201
rigid atoms, others: [2, 43, 44, 14, 15, 16, 17, 18, 53, 54, 26, 27] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 296
number of broken/clashed sets: 48
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040231 none CCC(=NNCC1=CC=C(OC)C=C1)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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 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]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 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: [18, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 9, 34, 34, 9, 12, 87, 113, 152, 152, 156, 179, 179, 34, 34, 18, 18, 18, 18, 18, 3, 1, 1, 1, 1, 3, 3, 3, 1, 1, 34, 34, 113, 113, 152, 152, 152, 152, 156, 156, 34, 34] 201
rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 12, 13, 41, 36, 42, 37] set([0, 1, 2, 3, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 695
number of broken/clashed sets: 48
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040231 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040231
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040231/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040231
Building REAL300000040232
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040232'
/scratch/stefan/7769621/working/building/REAL300000040232 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040232

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040232/0 /scratch/stefan/7769621/working/building/REAL300000040232 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 324)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/324
`/scratch/stefan/7769621/working/3D/324' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=C(C)C2=CSC(C(=O)[O-])=C2)C=C1)

`REAL300000040232.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040232.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040232/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040232 none COC1=CC=C(CNN=C(C)C2=CSC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', '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, 5, 1, 1, 14, 1, 1, 11, 11, 1, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 151, 201, 201, 142, 44, 12, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 201, 201, 201, 201, 142, 142, 44, 12, 12, 12, 1, 1, 201, 201] 201
rigid atoms, others: [32, 33, 9, 11, 12, 13, 14, 15, 18] 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, 31, 34, 35])
total number of confs: 852
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040232 none COC1=CC=C(CNN=C(C)C2=CSC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', '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, 5, 1, 1, 14, 1, 1, 11, 11, 1, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations 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, 45, 131, 131, 131, 201, 201, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 7, 7, 45, 132, 132, 132, 201, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 19, 20, 24, 25, 35] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 365
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040232 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040232
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040232/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040232
Building REAL300000040233
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040233'
/scratch/stefan/7769621/working/building/REAL300000040233 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040233

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040233/0 /scratch/stefan/7769621/working/building/REAL300000040233 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 325)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/325
`/scratch/stefan/7769621/working/3D/325' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=C2CC(C(=O)[O-])(C3=CC=CC=C3)C2)C=C1)

`REAL300000040233.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040233.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040233/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040233 none COC1=CC=C(CNN=C2CC(C(=O)[O-])(C3=CC=CC=C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', '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', '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, 12, 1, 1, 1, 1, 5, 8, 8, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 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, 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]
0  hydrogens need 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, 111, 201, 201, 111, 31, 6, 6, 6, 6, 1, 6, 9, 9, 1, 1, 1, 1, 1, 1, 6, 201, 201, 201, 201, 201, 201, 201, 111, 111, 31, 6, 6, 1, 1, 1, 1, 1, 6, 6, 201, 201] 201
rigid atoms, others: [34, 35, 36, 37, 38, 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, 33, 39, 40, 41, 42])
total number of confs: 888
number of broken/clashed sets: 170
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040233 none COC1=CC=C(CNN=C2CC(C(=O)[O-])(C3=CC=CC=C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', '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', '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, 12, 1, 1, 1, 1, 5, 8, 8, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 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, 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]
0  hydrogens 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, 132, 53, 139, 139, 53, 10, 1, 1, 1, 1, 1, 1, 3, 3, 1, 6, 6, 1, 6, 6, 1, 139, 139, 140, 140, 140, 139, 139, 53, 53, 10, 1, 1, 6, 6, 1, 6, 6, 1, 1, 139, 139] 201
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 15, 40, 21, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 41, 42])
total number of confs: 616
number of broken/clashed sets: 170
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040233 none COC1=CC=C(CNN=C2CC(C(=O)[O-])(C3=CC=CC=C3)C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', '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', '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, 12, 1, 1, 1, 1, 5, 8, 8, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 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, 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]
0  hydrogens need rotated
201  conformations 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, 43, 139, 139, 139, 139, 199, 199, 139, 201, 201, 139, 201, 201, 139, 1, 1, 2, 2, 2, 1, 1, 6, 6, 43, 139, 139, 201, 201, 139, 201, 201, 139, 139, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 42, 22, 23, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 786
number of broken/clashed sets: 170
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040233 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040233
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040233/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040233
Building REAL300000040234
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040234'
/scratch/stefan/7769621/working/building/REAL300000040234 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040234

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040234/0 /scratch/stefan/7769621/working/building/REAL300000040234 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 326)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/326
`/scratch/stefan/7769621/working/3D/326' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=C(C)[C@@H]2C[C@H](CC(=O)[O-])C2(C)C)C=C1)

`REAL300000040234.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040234.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040234/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040234 none COC1=CC=C(CNN=C(C)[C@@H]2C[C@H](CC(=O)[O-])C2(C)C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', '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', 'H', 'H', 'H', 'H', '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, 1, 5, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 1, 1, 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, 3, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [159, 159, 159, 159, 159, 88, 21, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 10, 10, 1, 1, 1, 159, 159, 159, 159, 159, 159, 159, 88, 88, 21, 5, 5, 5, 1, 1, 6, 6, 2, 2, 2, 2, 2, 2, 159, 159] 201
rigid atoms, others: [36, 37, 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, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 461
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040234 none COC1=CC=C(CNN=C(C)[C@@H]2C[C@H](CC(=O)[O-])C2(C)C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', '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', 'H', 'H', 'H', 'H', '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, 1, 5, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 1, 1, 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, 3, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 6, 39, 101, 101, 101, 159, 159, 159, 159, 159, 201, 201, 201, 159, 159, 159, 1, 1, 2, 2, 2, 1, 1, 6, 6, 39, 102, 102, 102, 159, 159, 201, 201, 159, 159, 159, 159, 159, 159, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 46, 47, 23, 24, 28, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 635
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040234 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040234
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040234/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040234
Building REAL300000040235
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040235'
/scratch/stefan/7769621/working/building/REAL300000040235 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040235

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040235/0 /scratch/stefan/7769621/working/building/REAL300000040235 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 327)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/327
`/scratch/stefan/7769621/working/3D/327' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=C(C)CCCCCCC(=O)[O-])C=C1)

`REAL300000040235.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040235.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040235/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040235 none COC1=CC=C(CNN=C(C)CCCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', '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, 12, 1, 1, 1, 1, 5, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 1, 1, 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, 3, 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, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 14, 28, 28, 28, 103, 120, 146, 144, 158, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 29, 29, 29, 103, 103, 136, 136, 143, 143, 158, 158, 162, 162, 199, 199, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 45, 46, 20, 21, 22, 23, 24, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 1123
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040235 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040235
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040235/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040235
Building REAL300000040236
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040236'
/scratch/stefan/7769621/working/building/REAL300000040236 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040236

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040236/0 /scratch/stefan/7769621/working/building/REAL300000040236 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 328)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/328
`/scratch/stefan/7769621/working/3D/328' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=C(C)C2=CC=C(OCCCC(=O)[O-])C(OC)=C2)C=C1)

`REAL300000040236.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040236.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040236/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040236 none COC1=CC=C(CNN=C(C)C2=CC=C(OCCCC(=O)[O-])C(OC)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 12, 1, 1, 1, 1, 5, 8, 8, 1, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 12, 5, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [63, 62, 36, 63, 63, 36, 17, 9, 9, 1, 9, 1, 1, 1, 1, 1, 8, 18, 20, 27, 33, 33, 1, 1, 3, 1, 63, 63, 63, 63, 63, 63, 63, 36, 36, 17, 9, 9, 9, 1, 1, 18, 18, 20, 20, 27, 27, 3, 3, 3, 1, 63, 63] 201
rigid atoms, others: [39, 40, 9, 11, 12, 13, 14, 15, 50, 22, 23, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 19, 20, 21, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52])
total number of confs: 456
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040236 none COC1=CC=C(CNN=C(C)C2=CC=C(OCCCC(=O)[O-])C(OC)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 12, 1, 1, 1, 1, 5, 8, 8, 1, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 12, 5, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 3, 7, 16, 16, 16, 63, 63, 63, 63, 132, 189, 192, 201, 201, 201, 63, 63, 101, 63, 1, 1, 2, 2, 2, 1, 1, 3, 3, 7, 17, 17, 17, 63, 63, 189, 189, 192, 192, 201, 201, 101, 101, 101, 63, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 51, 52, 26, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 652
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040236 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040236
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040236/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040236
Building REAL300000040237
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040237'
/scratch/stefan/7769621/working/building/REAL300000040237 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040237

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040237/0 /scratch/stefan/7769621/working/building/REAL300000040237 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 329)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/329
`/scratch/stefan/7769621/working/3D/329' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=C(C)C2=C(CC(=O)[O-])C3=CC=C(C)C=C3O2)C=C1)

`REAL300000040237.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040237.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040237/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040237 none COC1=CC=C(CNN=C(C)C2=C(CC(=O)[O-])C3=CC=C(C)C=C3O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 1, 1, 5, 8, 8, 1, 5, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 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, 4, 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]
0  hydrogens 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, 195, 152, 197, 197, 152, 43, 9, 9, 1, 9, 1, 1, 1, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 197, 197, 197, 197, 197, 197, 197, 152, 152, 42, 10, 10, 10, 2, 2, 1, 1, 2, 2, 2, 1, 197, 197] 201
rigid atoms, others: [40, 9, 11, 12, 13, 45, 17, 18, 19, 20, 41, 22, 23, 24, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 46, 47])
total number of confs: 855
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040237 none COC1=CC=C(CNN=C(C)C2=C(CC(=O)[O-])C3=CC=C(C)C=C3O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 1, 1, 5, 8, 8, 1, 5, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 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, 4, 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]
0  hydrogens need rotated
201  conformations 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, 42, 109, 109, 109, 197, 197, 201, 201, 201, 197, 197, 197, 197, 197, 197, 197, 197, 1, 1, 2, 2, 2, 1, 1, 7, 7, 42, 110, 110, 110, 201, 201, 197, 197, 197, 197, 197, 197, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 46, 47, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 377
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040237 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040237
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040237/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040237
Building REAL300000040238
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040238'
/scratch/stefan/7769621/working/building/REAL300000040238 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040238

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040238/0 /scratch/stefan/7769621/working/building/REAL300000040238 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 330)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/330
`/scratch/stefan/7769621/working/3D/330' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC(C(=O)[O-])=C(C)C=C2C)C=C1)

`REAL300000040238.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040238.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040238/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040238 none COC1=CC=C(CNN=CC2=CC(C(=O)[O-])=C(C)C=C2C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', '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, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 1, 1, 7, 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, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 127, 201, 201, 124, 45, 12, 12, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 124, 124, 45, 12, 1, 2, 2, 2, 1, 2, 2, 2, 201, 201] 201
rigid atoms, others: [32, 36, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 37, 38, 39, 40, 41])
total number of confs: 829
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040238 none COC1=CC=C(CNN=CC2=CC(C(=O)[O-])=C(C)C=C2C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', '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, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 1, 1, 7, 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, 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
201  conformations 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, 42, 113, 113, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 7, 7, 42, 113, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 40, 41, 21, 22, 23, 24, 25, 26, 27] set([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: 335
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040238 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040238
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040238/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040238
Building REAL300000040239
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040239'
/scratch/stefan/7769621/working/building/REAL300000040239 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040239

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040239/0 /scratch/stefan/7769621/working/building/REAL300000040239 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 331)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/331
`/scratch/stefan/7769621/working/3D/331' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=CC(C(=O)[O-])=C2Cl)C=C1)

`REAL300000040239.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040239.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040239/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040239 none COC1=CC=C(CNN=CC2=CC=CC(C(=O)[O-])=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', '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, 1, 1, 11, 11, 1, 16, 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, 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]
0  hydrogens need rotated
185  conformations in input
total number of sets (complete confs): 185
using faster count positions algorithm for large data
unique positions, atoms: [185, 168, 116, 185, 185, 116, 43, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 185, 185, 185, 185, 185, 185, 185, 116, 116, 43, 10, 1, 1, 1, 185, 185] 185
rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35])
total number of confs: 787
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040239 none COC1=CC=C(CNN=CC2=CC=CC(C(=O)[O-])=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', '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, 1, 1, 11, 11, 1, 16, 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, 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]
0  hydrogens need rotated
185  conformations in input
total number of sets (complete confs): 185
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 45, 149, 149, 185, 185, 185, 185, 185, 185, 185, 185, 185, 1, 1, 2, 2, 2, 1, 1, 7, 7, 45, 149, 185, 185, 185, 1, 1] 185
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 35, 20, 21, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 325
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040239 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040239
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040239/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040239
Building REAL300000040240
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040240'
/scratch/stefan/7769621/working/building/REAL300000040240 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040240

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040240/0 /scratch/stefan/7769621/working/building/REAL300000040240 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 332)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/332
`/scratch/stefan/7769621/working/3D/332' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)C=C1)

`REAL300000040240.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040240.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040240/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040240 none COC1=CC=C(CNN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 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, 7]
dock color type numbers: [7, 3, 7, 7, 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]
0  hydrogens need rotated
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, 180, 104, 76, 76, 48, 48, 48, 48, 48, 9, 3, 1, 3, 4, 4, 1, 1, 1, 1, 1, 1, 48, 201, 201, 201, 201, 201, 201, 201, 180, 180, 104, 76, 48, 48, 48, 3, 1, 1, 1, 1, 1, 48, 201, 201] 201
rigid atoms, others: [42, 43, 44, 45, 46, 16, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49])
total number of confs: 697
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: REAL300000040240 none COC1=CC=C(CNN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 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, 7]
dock color type numbers: [7, 3, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [42, 41, 37, 42, 42, 26, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 32, 46, 46, 32, 48, 48, 32, 48, 48, 1, 42, 42, 43, 43, 43, 42, 42, 26, 26, 10, 5, 1, 1, 1, 32, 48, 48, 32, 48, 48, 1, 42, 42] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 48, 49])
total number of confs: 393
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040240 none COC1=CC=C(CNN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 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, 7]
dock color type numbers: [7, 3, 7, 7, 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]
0  hydrogens need rotated
201  conformations 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, 14, 26, 26, 42, 42, 42, 42, 43, 116, 192, 201, 201, 192, 201, 201, 192, 201, 201, 42, 1, 1, 2, 2, 2, 1, 1, 6, 6, 14, 26, 42, 42, 42, 192, 201, 201, 192, 201, 201, 42, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 48, 49, 33, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 638
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040240 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040240
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040240/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040240
Building REAL300000040241
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040241'
/scratch/stefan/7769621/working/building/REAL300000040241 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040241

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040241/0 /scratch/stefan/7769621/working/building/REAL300000040241 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 333)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/333
`/scratch/stefan/7769621/working/3D/333' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=C(C(=O)[O-])C(F)=C2)C=C1)

`REAL300000040241.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040241.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040241/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040241 none COC1=CC=C(CNN=CC2=CC=C(C(=O)[O-])C(F)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', '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, 1, 11, 11, 1, 15, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [200, 195, 113, 200, 200, 107, 30, 6, 6, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 200, 200, 200, 200, 200, 200, 200, 107, 107, 30, 6, 1, 1, 1, 200, 200] 201
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])
total number of confs: 867
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040241 none COC1=CC=C(CNN=CC2=CC=C(C(=O)[O-])C(F)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', '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, 1, 11, 11, 1, 15, 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, 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]
0  hydrogens need rotated
201  conformations 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, 42, 113, 113, 200, 200, 200, 200, 201, 201, 200, 200, 200, 1, 1, 1, 1, 1, 1, 1, 7, 7, 42, 113, 200, 200, 200, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 35, 20, 21, 22, 23, 24, 25, 26] set([32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31])
total number of confs: 384
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040241 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040241
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040241/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040241
Building REAL300000040242
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040242'
/scratch/stefan/7769621/working/building/REAL300000040242 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040242

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040242/0 /scratch/stefan/7769621/working/building/REAL300000040242 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 334)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/334
`/scratch/stefan/7769621/working/3D/334' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=C(C=CC(=O)[O-])O2)C=C1)

`REAL300000040242.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040242.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040242/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040242 none COC1=CC=C(CNN=CC2=CC=C(C=CC(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', '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, 1, 1, 1, 11, 11, 12, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [129, 129, 93, 129, 129, 64, 18, 5, 5, 1, 1, 1, 1, 1, 1, 10, 10, 26, 26, 1, 129, 129, 129, 129, 129, 129, 129, 64, 64, 18, 5, 1, 1, 10, 10, 129, 129] 201
rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 19, 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, 30, 33, 34, 35, 36])
total number of confs: 517
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040242 none COC1=CC=C(CNN=CC2=CC=C(C=CC(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', '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, 1, 1, 1, 11, 11, 12, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations 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, 38, 102, 102, 129, 129, 129, 129, 201, 201, 201, 201, 129, 1, 1, 1, 1, 1, 1, 1, 6, 6, 38, 102, 129, 129, 201, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 35, 20, 21, 22, 23, 24, 25, 26, 36] set([32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31])
total number of confs: 480
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040242 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040242
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040242/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040242
Building REAL300000040243
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040243'
/scratch/stefan/7769621/working/building/REAL300000040243 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040243

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040243/0 /scratch/stefan/7769621/working/building/REAL300000040243 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 335)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/335
`/scratch/stefan/7769621/working/3D/335' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CNC3=CC=C(C(=O)[O-])C=C23)C=C1)

`REAL300000040243.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040243.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040243/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040243 none COC1=CC=C(CNN=CC2=CNC3=CC=C(C(=O)[O-])C=C23)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 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]
0  hydrogens need rotated
154  conformations in input
total number of sets (complete confs): 154
using faster count positions algorithm for large data
unique positions, atoms: [154, 154, 121, 154, 154, 121, 43, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 154, 154, 154, 154, 154, 154, 154, 121, 121, 43, 9, 1, 1, 1, 1, 1, 154, 154] 154
rigid atoms, others: [33, 34, 35, 36, 37, 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, 32, 38, 39])
total number of confs: 608
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040243 none COC1=CC=C(CNN=CC2=CNC3=CC=C(C(=O)[O-])C=C23)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 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]
0  hydrogens need rotated
154  conformations in input
total number of sets (complete confs): 154
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 42, 125, 125, 154, 154, 154, 154, 154, 154, 154, 154, 154, 154, 154, 1, 1, 2, 2, 2, 1, 1, 7, 7, 42, 125, 154, 154, 154, 154, 154, 1, 1] 154
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 38, 22, 23, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 282
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040243 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040243
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040243/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040243
Building REAL300000040244
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040244'
/scratch/stefan/7769621/working/building/REAL300000040244 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040244

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040244/0 /scratch/stefan/7769621/working/building/REAL300000040244 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 336)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/336
`/scratch/stefan/7769621/working/3D/336' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC(Cl)=C(OC(C)C(=O)[O-])C(OC)=C2)C=C1)

`REAL300000040244.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040244.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040244/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040244 none COC1=CC=C(CNN=CC2=CC(Cl)=C(OC(C)C(=O)[O-])C(OC)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 1, 12, 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, 3, 7, 7, 7, 7, 7, 4, 7, 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]
0  hydrogens 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, 97, 68, 121, 121, 68, 17, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 11, 11, 16, 16, 1, 1, 3, 1, 121, 121, 122, 122, 122, 122, 122, 69, 69, 17, 6, 1, 11, 12, 12, 12, 4, 4, 4, 1, 122, 122] 201
rigid atoms, others: [36, 9, 10, 11, 12, 13, 14, 15, 21, 22, 24, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 45, 46])
total number of confs: 622
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040244 none COC1=CC=C(CNN=CC2=CC(Cl)=C(OC(C)C(=O)[O-])C(OC)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 1, 12, 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, 3, 7, 7, 7, 7, 7, 4, 7, 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]
0  hydrogens need rotated
201  conformations 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, 34, 61, 61, 121, 121, 121, 121, 121, 189, 200, 199, 201, 201, 121, 121, 158, 121, 1, 1, 2, 2, 2, 1, 1, 6, 6, 34, 61, 121, 199, 200, 200, 200, 158, 158, 158, 121, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 45, 46, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 468
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040244 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040244
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040244/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040244
Building REAL300000040245
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040245'
/scratch/stefan/7769621/working/building/REAL300000040245 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040245

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040245/0 /scratch/stefan/7769621/working/building/REAL300000040245 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 337)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/337
`/scratch/stefan/7769621/working/3D/337' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=C(C(=O)[O-])C(O)=C2)C=C1)

`REAL300000040245.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040245.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040245/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040245 none COC1=CC=C(CNN=CC2=CC=C(C(=O)[O-])C(O)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', '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, 1, 11, 11, 1, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 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]
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, 128, 201, 201, 128, 46, 9, 9, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 128, 128, 46, 9, 1, 1, 2, 1, 201, 201] 402
rigid atoms, others: [32, 34, 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, 33, 35, 36])
total number of confs: 867
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040245 none COC1=CC=C(CNN=CC2=CC=C(C(=O)[O-])C(O)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', '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, 1, 11, 11, 1, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 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]
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, 7, 45, 131, 131, 201, 201, 200, 200, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 7, 7, 45, 131, 201, 201, 402, 201, 1, 1] 402
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 35, 20, 21, 22, 23, 24, 25, 26, 36] set([32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31])
total number of confs: 781
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040245 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040245
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040245/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040245
Building REAL300000040246
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040246'
/scratch/stefan/7769621/working/building/REAL300000040246 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040246

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040246/0 /scratch/stefan/7769621/working/building/REAL300000040246 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 338)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/338
`/scratch/stefan/7769621/working/3D/338' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC(C(=O)[O-])=C(Cl)S2)C=C1)

`REAL300000040246.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040246.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040246/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040246 none COC1=CC=C(CNN=CC2=CC(C(=O)[O-])=C(Cl)S2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 1, 1, 7, 7, 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, 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: [200, 200, 130, 200, 200, 98, 34, 8, 8, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 200, 200, 200, 200, 201, 200, 200, 98, 98, 34, 8, 1, 200, 200] 201
rigid atoms, others: [9, 10, 11, 12, 13, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32])
total number of confs: 741
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040246 none COC1=CC=C(CNN=CC2=CC(C(=O)[O-])=C(Cl)S2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 1, 1, 7, 7, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 36, 118, 118, 200, 200, 200, 201, 201, 200, 200, 200, 1, 1, 1, 1, 1, 1, 1, 6, 6, 36, 118, 200, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 19, 20, 21, 22, 23, 24, 25, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30])
total number of confs: 358
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040246 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040246
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040246/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040246
Building REAL300000040247
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040247'
/scratch/stefan/7769621/working/building/REAL300000040247 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040247

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040247/0 /scratch/stefan/7769621/working/building/REAL300000040247 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 339)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/339
`/scratch/stefan/7769621/working/3D/339' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)C=C1)

`REAL300000040247.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040247.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040247/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040247 none COC1=CC=C(CNN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 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]
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, 191, 201, 201, 164, 80, 32, 32, 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, 80, 32, 12, 12, 1, 1, 2, 1, 201, 201] 402
rigid atoms, others: [38, 39, 41, 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, 37, 40, 42, 43])
total number of confs: 701
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: REAL300000040247 none COC1=CC=C(CNN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 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]
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: [121, 120, 84, 121, 121, 56, 19, 6, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 13, 13, 12, 1, 121, 121, 121, 121, 121, 121, 121, 56, 56, 19, 6, 1, 1, 12, 12, 24, 12, 121, 120] 402
rigid atoms, others: [36, 37, 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, 35, 38, 39, 40, 41, 42, 43])
total number of confs: 483
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040247 none COC1=CC=C(CNN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 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]
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, 6, 32, 84, 84, 121, 121, 121, 121, 201, 201, 201, 201, 201, 201, 201, 201, 201, 121, 1, 1, 1, 1, 1, 1, 1, 6, 6, 32, 84, 121, 121, 201, 201, 402, 201, 1, 1] 402
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 43, 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])
total number of confs: 751
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040247 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040247
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040247/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040247
Building REAL300000040248
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040248'
/scratch/stefan/7769621/working/building/REAL300000040248 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040248

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040248/0 /scratch/stefan/7769621/working/building/REAL300000040248 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 340)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/340
`/scratch/stefan/7769621/working/3D/340' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC(C(=O)[O-])=CC=C2N(C)C)C=C1)

`REAL300000040248.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040248.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040248/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040248 none COC1=CC=C(CNN=CC2=CC(C(=O)[O-])=CC=C2N(C)C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.pl3', '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, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 5, 5, 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, 3, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
119  conformations in input
total number of sets (complete confs): 119
using faster count positions algorithm for large data
unique positions, atoms: [119, 119, 99, 119, 119, 94, 30, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 119, 119, 119, 119, 119, 119, 119, 94, 94, 30, 5, 1, 1, 1, 4, 4, 4, 3, 3, 3, 119, 119] 119
rigid atoms, others: [33, 34, 35, 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, 32, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 466
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040248 none COC1=CC=C(CNN=CC2=CC(C(=O)[O-])=CC=C2N(C)C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.pl3', '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, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 5, 5, 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, 3, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
119  conformations in input
total number of sets (complete confs): 119
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 43, 104, 104, 119, 119, 119, 119, 119, 119, 119, 119, 119, 119, 119, 1, 1, 1, 1, 1, 1, 1, 8, 8, 43, 104, 119, 119, 119, 119, 119, 119, 119, 119, 119, 1, 1] 119
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 43, 22, 23, 24, 25, 26, 27, 28] set([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])
total number of confs: 229
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040248 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040248
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040248/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040248
Building REAL300000040249
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040249'
/scratch/stefan/7769621/working/building/REAL300000040249 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040249

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040249/0 /scratch/stefan/7769621/working/building/REAL300000040249 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 341)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/341
`/scratch/stefan/7769621/working/3D/341' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)C=C1)

`REAL300000040249.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040249.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040249/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040249 none COC1=CC=C(CNN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 173, 201, 201, 173, 85, 42, 42, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 201, 201, 201, 201, 201, 201, 201, 173, 173, 85, 42, 12, 12, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [37, 38, 39, 40, 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, 36, 41, 42])
total number of confs: 784
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: REAL300000040249 none COC1=CC=C(CNN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 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]
0  hydrogens 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, 100, 61, 103, 103, 53, 18, 6, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 1, 103, 103, 104, 104, 104, 104, 104, 54, 54, 18, 6, 1, 1, 12, 12, 12, 12, 104, 104] 201
rigid atoms, others: [35, 36, 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, 34, 37, 38, 39, 40, 41, 42])
total number of confs: 436
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040249 none COC1=CC=C(CNN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations 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, 30, 66, 66, 103, 103, 103, 103, 201, 201, 201, 201, 201, 201, 201, 201, 103, 1, 1, 2, 2, 2, 1, 1, 6, 6, 30, 66, 103, 103, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 42, 24, 25, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 354
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040249 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040249
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040249/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040249
Building REAL300000040250
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040250'
/scratch/stefan/7769621/working/building/REAL300000040250 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040250

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040250/0 /scratch/stefan/7769621/working/building/REAL300000040250 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 342)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/342
`/scratch/stefan/7769621/working/3D/342' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC(C(=O)[O-])=CC=C2OC)C=C1)

`REAL300000040250.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040250.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040250/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040250 none COC1=CC=C(CNN=CC2=CC(C(=O)[O-])=CC=C2OC)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.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: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 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]
0  hydrogens need 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, 110, 201, 201, 107, 36, 6, 6, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 3, 201, 201, 201, 201, 201, 201, 201, 107, 107, 36, 6, 1, 1, 1, 3, 3, 3, 201, 201] 201
rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39])
total number of confs: 837
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040250 none COC1=CC=C(CNN=CC2=CC(C(=O)[O-])=CC=C2OC)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.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: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations 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, 41, 132, 132, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 6, 6, 41, 132, 201, 201, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 38, 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])
total number of confs: 358
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040250 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040250
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040250/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040250
Building REAL300000040251
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040251'
/scratch/stefan/7769621/working/building/REAL300000040251 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040251

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040251/0 /scratch/stefan/7769621/working/building/REAL300000040251 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 343)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/343
`/scratch/stefan/7769621/working/3D/343' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)C=C1)

`REAL300000040251.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040251.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040251/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040251 none COC1=CC=C(CNN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 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, 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]
0  hydrogens need rotated
157  conformations in input
total number of sets (complete confs): 157
using faster count positions algorithm for large data
unique positions, atoms: [157, 157, 127, 157, 157, 127, 41, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 157, 157, 157, 157, 157, 157, 157, 127, 127, 41, 10, 1, 1, 1, 1, 157, 157] 157
rigid atoms, others: [33, 34, 35, 36, 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, 32, 37, 38])
total number of confs: 601
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040251 none COC1=CC=C(CNN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 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, 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]
0  hydrogens need rotated
157  conformations in input
total number of sets (complete confs): 157
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 41, 127, 127, 157, 157, 157, 157, 157, 157, 157, 157, 157, 157, 157, 1, 1, 1, 1, 1, 1, 1, 6, 6, 41, 127, 157, 157, 157, 157, 1, 1] 157
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 38, 22, 23, 24, 25, 26, 27, 28, 37] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 279
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040251 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040251
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040251/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040251
Building REAL300000040252
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040252'
/scratch/stefan/7769621/working/building/REAL300000040252 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040252

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040252/0 /scratch/stefan/7769621/working/building/REAL300000040252 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 344)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/344
`/scratch/stefan/7769621/working/3D/344' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC(C(=O)[O-])=CC=C2Br)C=C1)

`REAL300000040252.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040252.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040252/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040252 none COC1=CC=C(CNN=CC2=CC(C(=O)[O-])=CC=C2Br)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 146, 201, 201, 146, 66, 12, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 146, 146, 66, 12, 1, 1, 1, 201, 201] 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])
total number of confs: 835
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040252 none COC1=CC=C(CNN=CC2=CC(C(=O)[O-])=CC=C2Br)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 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, 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]
0  hydrogens need rotated
201  conformations 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, 40, 113, 113, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 6, 6, 40, 113, 201, 201, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 35, 20, 21, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 352
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040252 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040252
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040252/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040252
Building REAL300000040253
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040253'
/scratch/stefan/7769621/working/building/REAL300000040253 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040253

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040253/0 /scratch/stefan/7769621/working/building/REAL300000040253 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 345)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/345
`/scratch/stefan/7769621/working/3D/345' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=C(C(=O)[O-])C(OC)=C2)C=C1)

`REAL300000040253.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040253.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040253/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040253 none COC1=CC=C(CNN=CC2=CC=C(C(=O)[O-])C(OC)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', '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, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [157, 157, 77, 157, 157, 77, 28, 7, 7, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 1, 157, 157, 157, 157, 157, 157, 157, 77, 77, 28, 7, 1, 1, 3, 3, 3, 1, 157, 157] 201
rigid atoms, others: [32, 33, 37, 9, 10, 11, 12, 13, 14, 17, 18, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 38, 39])
total number of confs: 692
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040253 none COC1=CC=C(CNN=CC2=CC=C(C(=O)[O-])C(OC)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', '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, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations 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, 36, 87, 87, 157, 157, 156, 156, 201, 201, 157, 157, 201, 157, 1, 1, 2, 2, 2, 1, 1, 6, 6, 36, 87, 157, 157, 201, 201, 201, 157, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 38, 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])
total number of confs: 567
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040253 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040253
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040253/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040253
Building REAL300000040254
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040254'
/scratch/stefan/7769621/working/building/REAL300000040254 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040254

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040254/0 /scratch/stefan/7769621/working/building/REAL300000040254 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 346)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/346
`/scratch/stefan/7769621/working/3D/346' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=C(F)C=C(C(=O)[O-])C=C2F)C=C1)

`REAL300000040254.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040254.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040254/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040254 none COC1=CC=C(CNN=CC2=C(F)C=C(C(=O)[O-])C=C2F)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', '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, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 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, 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]
0  hydrogens need rotated
139  conformations in input
total number of sets (complete confs): 139
using faster count positions algorithm for large data
unique positions, atoms: [139, 139, 103, 139, 139, 103, 52, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 139, 139, 139, 139, 139, 139, 139, 103, 103, 52, 8, 1, 1, 139, 139] 139
rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 575
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040254 none COC1=CC=C(CNN=CC2=C(F)C=C(C(=O)[O-])C=C2F)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', '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, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 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, 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]
0  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 41, 125, 125, 138, 138, 138, 128, 138, 138, 138, 138, 138, 138, 1, 1, 2, 2, 2, 1, 1, 6, 6, 41, 125, 138, 138, 1, 1] 138
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 35, 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])
total number of confs: 302
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040254 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040254
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040254/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040254
Building REAL300000040255
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040255'
/scratch/stefan/7769621/working/building/REAL300000040255 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040255

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040255/0 /scratch/stefan/7769621/working/building/REAL300000040255 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 347)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/347
`/scratch/stefan/7769621/working/3D/347' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC(C(=O)[O-])=CC(Br)=C2O)C=C1)

`REAL300000040255.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040255.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040255/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040255 none COC1=CC=C(CNN=CC2=CC(C(=O)[O-])=CC(Br)=C2O)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 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]
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, 201, 151, 60, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 151, 151, 60, 13, 1, 1, 2, 201, 201] 402
rigid atoms, others: [32, 33, 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, 34, 35, 36])
total number of confs: 816
number of broken/clashed sets: 61
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040255 none COC1=CC=C(CNN=CC2=CC(C(=O)[O-])=CC(Br)=C2O)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 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]
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, 8, 47, 125, 125, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 8, 8, 47, 125, 201, 201, 402, 1, 1] 402
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 35, 21, 22, 23, 24, 25, 26, 27, 36] set([32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31])
total number of confs: 756
number of broken/clashed sets: 61
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040255 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040255/1 /scratch/stefan/7769621/working/building/REAL300000040255 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 348)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/348
`/scratch/stefan/7769621/working/3D/348' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC(C(=O)[O-])=CC(Br)=C2[O-])C=C1)

`REAL300000040255.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040255.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040255/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040255 none COC1=CC=C(CNN=CC2=CC(C(=O)[O-])=CC(Br)=C2[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 1, 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, 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]
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, 117, 92, 117, 117, 91, 36, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 117, 117, 117, 91, 91, 36, 6, 1, 1, 117, 117] 117
rigid atoms, others: [32, 33, 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, 34, 35])
total number of confs: 479
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040255 none COC1=CC=C(CNN=CC2=CC(C(=O)[O-])=CC(Br)=C2[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 1, 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, 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]
0  hydrogens need rotated
117  conformations in input
total number of sets (complete confs): 117
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 36, 95, 95, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 1, 1, 2, 2, 2, 1, 1, 7, 7, 36, 95, 117, 117, 1, 1] 117
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 35, 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])
total number of confs: 234
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040255 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040255
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040255/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040255/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040255
Building REAL300000040256
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040256'
/scratch/stefan/7769621/working/building/REAL300000040256 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040256

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040256/0 /scratch/stefan/7769621/working/building/REAL300000040256 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 349)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/349
`/scratch/stefan/7769621/working/3D/349' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)C=C1)

`REAL300000040256.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040256.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040256/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040256 none COC1=CC=C(CNN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 1, 1, 7, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 165, 201, 201, 165, 76, 34, 34, 17, 17, 17, 17, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 201, 201, 201, 201, 201, 201, 201, 165, 165, 76, 34, 17, 17, 9, 9, 1, 1, 17, 17, 201, 201] 201
rigid atoms, others: [41, 42, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46])
total number of confs: 820
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: REAL300000040256 none COC1=CC=C(CNN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 1, 1, 7, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [97, 86, 40, 97, 97, 40, 12, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 17, 17, 17, 17, 17, 17, 17, 1, 1, 97, 97, 97, 97, 97, 97, 97, 40, 40, 12, 4, 1, 1, 2, 2, 17, 17, 1, 1, 97, 97] 201
rigid atoms, others: [43, 37, 38, 9, 10, 11, 12, 13, 14, 44, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 45, 46])
total number of confs: 447
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040256 none COC1=CC=C(CNN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 1, 1, 7, 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, 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]
0  hydrogens need rotated
201  conformations 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, 40, 78, 78, 97, 97, 79, 97, 149, 149, 201, 201, 201, 201, 201, 201, 201, 97, 97, 1, 1, 1, 1, 1, 1, 1, 6, 6, 40, 78, 97, 97, 149, 149, 201, 201, 97, 97, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 45, 46, 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, 25, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 487
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040256 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040256
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040256/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040256
Building REAL300000040257
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040257'
/scratch/stefan/7769621/working/building/REAL300000040257 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040257

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040257/0 /scratch/stefan/7769621/working/building/REAL300000040257 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 350)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/350
`/scratch/stefan/7769621/working/3D/350' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)C=C1)

`REAL300000040257.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040257.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040257/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040257 none COC1=CC=C(CNN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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]
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, 156, 201, 201, 156, 57, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 156, 156, 57, 11, 2, 1, 1, 1, 1, 1, 201, 201] 402
rigid atoms, others: [36, 37, 38, 39, 40, 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, 35, 41, 42])
total number of confs: 805
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040257 none COC1=CC=C(CNN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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]
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, 8, 44, 143, 143, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 8, 8, 44, 143, 402, 201, 201, 201, 201, 201, 1, 1] 402
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 42, 24, 25, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 765
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040257 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040257
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040257/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040257
Building REAL300000040258
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040258'
/scratch/stefan/7769621/working/building/REAL300000040258 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040258

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040258/0 /scratch/stefan/7769621/working/building/REAL300000040258 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 351)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/351
`/scratch/stefan/7769621/working/3D/351' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)C=C1)

`REAL300000040258.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040258.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040258/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040258 none COC1=CC=C(CNN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 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, 7]
dock color type numbers: [7, 3, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [162, 162, 140, 162, 162, 112, 33, 11, 11, 1, 2, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 5, 5, 162, 162, 162, 162, 162, 162, 162, 112, 112, 33, 11, 5, 5, 1, 1, 1, 2, 2, 1, 5, 5, 162, 162] 201
rigid atoms, others: [39, 40, 41, 44, 13, 14, 15, 16, 17, 18, 19, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 45, 46, 47, 48])
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: REAL300000040258 none COC1=CC=C(CNN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 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, 7]
dock color type numbers: [7, 3, 7, 7, 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]
0  hydrogens 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, 80, 64, 81, 81, 44, 12, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 23, 23, 5, 1, 1, 81, 81, 82, 82, 82, 82, 82, 45, 45, 11, 3, 1, 1, 5, 5, 5, 9, 9, 5, 1, 1, 82, 82] 201
rigid atoms, others: [37, 38, 9, 10, 11, 12, 13, 14, 45, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 47, 48])
total number of confs: 370
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040258 none COC1=CC=C(CNN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 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, 7]
dock color type numbers: [7, 3, 7, 7, 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]
0  hydrogens need rotated
201  conformations 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, 30, 61, 61, 81, 81, 61, 61, 162, 162, 162, 162, 162, 201, 201, 201, 162, 81, 81, 1, 1, 2, 2, 2, 1, 1, 6, 6, 30, 61, 82, 82, 162, 162, 162, 201, 201, 162, 82, 81, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 47, 48, 26, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 622
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040258 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040258
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040258/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040258
Building REAL300000040259
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040259'
/scratch/stefan/7769621/working/building/REAL300000040259 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040259

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040259/0 /scratch/stefan/7769621/working/building/REAL300000040259 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 352)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/352
`/scratch/stefan/7769621/working/3D/352' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC(C=NNCC2=CC=C(OC)C=C2)=CC=C1OCC(=O)[O-])

`REAL300000040259.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040259.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040259/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040259 none CCOC1=CC(C=NNCC2=CC=C(OC)C=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.3', '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.2', '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, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 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, 7, 7, 7]
0  hydrogens 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, 95, 43, 43, 43, 19, 19, 9, 3, 1, 1, 1, 1, 1, 1, 2, 1, 1, 42, 42, 42, 42, 128, 187, 191, 191, 104, 104, 104, 104, 104, 43, 19, 9, 3, 3, 1, 1, 3, 3, 3, 1, 1, 42, 42, 187, 187] 201
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, 43, 44, 45, 46])
total number of confs: 665
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040259 none CCOC1=CC(C=NNCC2=CC=C(OC)C=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.3', '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.2', '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, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 7, 1, 1, 1, 1, 1, 6, 6, 15, 37, 43, 43, 40, 43, 71, 43, 43, 1, 1, 1, 1, 7, 25, 35, 35, 12, 12, 12, 12, 12, 1, 6, 14, 37, 37, 43, 43, 71, 71, 71, 43, 43, 1, 1, 25, 25] 201
rigid atoms, others: [2, 3, 4, 5, 6, 43, 44, 18, 19, 20, 21, 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, 37, 38, 39, 40, 41, 42, 45, 46])
total number of confs: 357
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040259 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040259
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040259/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040259
Building REAL300000040260
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040260'
/scratch/stefan/7769621/working/building/REAL300000040260 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040260

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040260/0 /scratch/stefan/7769621/working/building/REAL300000040260 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 353)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/353
`/scratch/stefan/7769621/working/3D/353' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=C(CCC(=O)[O-])O2)C=C1)

`REAL300000040260.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040260.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040260/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040260 none COC1=CC=C(CNN=CC2=CC=C(CCC(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', '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, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 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: [104, 98, 51, 104, 104, 44, 16, 5, 5, 1, 1, 1, 1, 1, 1, 8, 12, 21, 13, 1, 104, 104, 104, 104, 104, 104, 104, 44, 44, 16, 5, 1, 1, 8, 8, 12, 12, 104, 102] 201
rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 19, 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, 30, 33, 34, 35, 36, 37, 38])
total number of confs: 493
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040260 none COC1=CC=C(CNN=CC2=CC=C(CCC(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', '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, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 6, 36, 81, 81, 104, 104, 104, 104, 187, 201, 201, 196, 104, 1, 1, 1, 1, 1, 1, 1, 6, 6, 36, 81, 104, 104, 187, 187, 201, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 38, 37] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 726
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040260 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040260
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040260/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040260
Building REAL300000040261
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040261'
/scratch/stefan/7769621/working/building/REAL300000040261 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040261

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040261/0 /scratch/stefan/7769621/working/building/REAL300000040261 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 354)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/354
`/scratch/stefan/7769621/working/3D/354' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CNC3=C(C(=O)[O-])C=CC=C23)C=C1)

`REAL300000040261.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040261.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040261/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040261 none COC1=CC=C(CNN=CC2=CNC3=C(C(=O)[O-])C=CC=C23)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', '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, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 199, 147, 200, 200, 144, 51, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 200, 200, 201, 201, 201, 201, 201, 145, 145, 51, 10, 1, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [33, 34, 35, 36, 37, 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, 32, 38, 39])
total number of confs: 830
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040261 none COC1=CC=C(CNN=CC2=CNC3=C(C(=O)[O-])C=CC=C23)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', '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, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 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]
0  hydrogens need rotated
201  conformations 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, 44, 148, 148, 200, 200, 200, 200, 200, 201, 201, 200, 200, 200, 200, 1, 1, 1, 1, 1, 1, 1, 6, 6, 44, 148, 200, 200, 200, 201, 200, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 38, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 359
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040261 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040261
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040261/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040261
Building REAL300000040262
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040262'
/scratch/stefan/7769621/working/building/REAL300000040262 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040262

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040262/0 /scratch/stefan/7769621/working/building/REAL300000040262 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 355)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/355
`/scratch/stefan/7769621/working/3D/355' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)C=C1)

`REAL300000040262.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040262.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040262/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040262 none COC1=CC=C(CNN=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 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, 3, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 183, 201, 201, 143, 51, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 143, 143, 51, 10, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [33, 34, 35, 36, 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, 32, 37, 38])
total number of confs: 687
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040262 none COC1=CC=C(CNN=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 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, 3, 7, 7, 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]
0  hydrogens need rotated
201  conformations 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, 45, 141, 141, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 7, 7, 45, 141, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 38, 22, 23, 27, 28, 37] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 369
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040262 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040262
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040262/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040262
Building REAL300000040263
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040263'
/scratch/stefan/7769621/working/building/REAL300000040263 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040263

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040263/0 /scratch/stefan/7769621/working/building/REAL300000040263 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 356)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/356
`/scratch/stefan/7769621/working/3D/356' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=CN3C(C(=O)[O-])=CN=C23)C=C1)

`REAL300000040263.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040263.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040263/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040263 none COC1=CC=C(CNN=CC2=CC=CN3C(C(=O)[O-])=CN=C23)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 1, 1, 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, 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]
0  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [138, 138, 120, 138, 138, 100, 36, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 138, 138, 138, 138, 138, 138, 138, 100, 100, 36, 6, 1, 1, 1, 1, 138, 138] 138
rigid atoms, others: [33, 34, 35, 36, 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, 32, 37, 38])
total number of confs: 498
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040263 none COC1=CC=C(CNN=CC2=CC=CN3C(C(=O)[O-])=CN=C23)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 1, 1, 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, 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]
0  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 48, 116, 116, 138, 138, 138, 138, 138, 138, 138, 138, 138, 138, 138, 1, 1, 2, 2, 2, 1, 1, 7, 7, 48, 116, 138, 138, 138, 138, 1, 1] 138
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 38, 22, 23, 27, 28, 37] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 272
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040263 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040263
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040263/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040263
Building REAL300000040264
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040264'
/scratch/stefan/7769621/working/building/REAL300000040264 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040264

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040264/0 /scratch/stefan/7769621/working/building/REAL300000040264 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 357)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/357
`/scratch/stefan/7769621/working/3D/357' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)C=C1)

`REAL300000040264.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040264.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040264/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040264 none COC1=CC=C(CNN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 191, 201, 201, 186, 114, 97, 97, 81, 81, 81, 81, 81, 81, 39, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 186, 186, 114, 97, 81, 81, 81, 81, 9, 9, 1, 1, 201, 201] 201
rigid atoms, others: [43, 44, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46])
total number of confs: 718
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: REAL300000040264 none COC1=CC=C(CNN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [50, 50, 31, 50, 50, 25, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 27, 81, 81, 81, 81, 81, 81, 81, 50, 50, 50, 50, 50, 50, 50, 25, 25, 10, 4, 1, 1, 1, 1, 27, 27, 81, 81, 50, 50] 201
rigid atoms, others: [37, 38, 39, 40, 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, 36, 41, 42, 43, 44, 45, 46])
total number of confs: 360
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040264 none COC1=CC=C(CNN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 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, 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]
0  hydrogens need rotated
201  conformations 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, 4, 18, 36, 36, 50, 50, 50, 50, 50, 50, 98, 151, 201, 201, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 4, 4, 18, 36, 50, 50, 50, 50, 151, 151, 201, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 45, 46, 26, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 510
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040264 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040264
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040264/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040264
Building REAL300000040265
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040265'
/scratch/stefan/7769621/working/building/REAL300000040265 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040265

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040265/0 /scratch/stefan/7769621/working/building/REAL300000040265 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 358)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/358
`/scratch/stefan/7769621/working/3D/358' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)C=C1)

`REAL300000040265.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040265.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040265/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040265 none COC1=CC=C(CNN=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [85, 85, 45, 85, 85, 45, 15, 7, 7, 1, 1, 1, 1, 1, 1, 7, 28, 36, 36, 1, 1, 1, 85, 85, 85, 85, 85, 85, 85, 45, 45, 15, 7, 1, 1, 28, 28, 1, 85, 85] 201
rigid atoms, others: [33, 34, 37, 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, 32, 35, 36, 38, 39])
total number of confs: 501
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040265 none COC1=CC=C(CNN=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations 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, 22, 44, 44, 85, 85, 65, 83, 177, 201, 201, 201, 85, 85, 85, 1, 1, 2, 2, 2, 1, 1, 6, 6, 22, 44, 85, 85, 201, 201, 85, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 38, 22, 23, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 526
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040265 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040265
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040265/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040265
Building REAL300000040266
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040266'
/scratch/stefan/7769621/working/building/REAL300000040266 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040266

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040266/0 /scratch/stefan/7769621/working/building/REAL300000040266 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 359)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/359
`/scratch/stefan/7769621/working/3D/359' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)C=C1)

`REAL300000040266.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040266.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040266/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040266 none COC1=CC=C(CNN=CC2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [85, 85, 60, 85, 85, 38, 10, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 30, 46, 46, 1, 1, 85, 85, 85, 85, 85, 85, 85, 38, 38, 10, 4, 1, 1, 9, 30, 30, 1, 1, 85, 85] 201
rigid atoms, others: [35, 36, 40, 9, 10, 11, 12, 13, 14, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 42, 43])
total number of confs: 482
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040266 none COC1=CC=C(CNN=CC2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens need rotated
201  conformations 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, 23, 46, 46, 85, 85, 46, 47, 105, 105, 105, 163, 201, 201, 201, 85, 85, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 46, 85, 85, 163, 201, 201, 85, 85, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 43, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 963
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040266 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040266
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040266/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040266
Building REAL300000040267
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040267'
/scratch/stefan/7769621/working/building/REAL300000040267 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040267

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040267/0 /scratch/stefan/7769621/working/building/REAL300000040267 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 360)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/360
`/scratch/stefan/7769621/working/3D/360' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)C=C1)

`REAL300000040267.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040267.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040267/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040267 none COC1=CC=C(CNN=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 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, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 164, 201, 201, 164, 64, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 164, 164, 64, 12, 1, 1, 1, 201, 201] 201
rigid atoms, others: [34, 35, 36, 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, 33, 37, 38])
total number of confs: 809
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040267 none COC1=CC=C(CNN=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 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, 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
201  conformations 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, 46, 132, 132, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 7, 7, 46, 132, 201, 201, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 38, 28, 29, 37] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 360
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040267 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040267
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040267/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040267
Building REAL300000040268
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040268'
/scratch/stefan/7769621/working/building/REAL300000040268 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040268

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040268/0 /scratch/stefan/7769621/working/building/REAL300000040268 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 361)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/361
`/scratch/stefan/7769621/working/3D/361' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=CC=C(C(=O)[O-])C=C2OC)C=C1)

`REAL300000040268.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040268.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040268/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040268 none COC1=CC=C(CNN=CC2=CC=C(C(=O)[O-])C=C2OC)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', '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, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 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]
0  hydrogens need rotated
195  conformations in input
total number of sets (complete confs): 195
using faster count positions algorithm for large data
unique positions, atoms: [195, 189, 116, 195, 195, 116, 35, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3, 195, 195, 195, 195, 195, 195, 195, 116, 116, 35, 6, 1, 1, 1, 3, 3, 3, 195, 195] 195
rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39])
total number of confs: 825
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040268 none COC1=CC=C(CNN=CC2=CC=C(C(=O)[O-])C=C2OC)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', '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, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 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]
0  hydrogens need rotated
195  conformations in input
total number of sets (complete confs): 195
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 50, 168, 168, 195, 195, 195, 195, 195, 195, 195, 195, 195, 195, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 168, 195, 195, 195, 195, 195, 195, 1, 1] 195
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 38, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 337
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040268 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040268
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040268/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040268
Building REAL300000040269
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040269'
/scratch/stefan/7769621/working/building/REAL300000040269 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040269

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040269/0 /scratch/stefan/7769621/working/building/REAL300000040269 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 362)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/362
`/scratch/stefan/7769621/working/3D/362' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CNN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)C=C1)

`REAL300000040269.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040269.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040269/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040269 none COC1=CC=C(CNN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 200, 137, 201, 201, 132, 58, 23, 23, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 12, 12, 201, 201, 201, 201, 201, 201, 201, 132, 132, 58, 23, 1, 1, 1, 1, 12, 12, 201, 201] 201
rigid atoms, others: [35, 36, 37, 38, 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, 39, 40, 41, 42])
total number of confs: 840
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: REAL300000040269 none COC1=CC=C(CNN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [85, 84, 37, 85, 85, 36, 12, 4, 4, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 23, 23, 12, 1, 1, 85, 85, 85, 85, 85, 85, 85, 36, 36, 12, 4, 12, 12, 12, 12, 1, 1, 85, 85] 201
rigid atoms, others: [39, 40, 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, 38, 41, 42])
total number of confs: 427
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040269 none COC1=CC=C(CNN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 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
201  conformations 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, 35, 72, 72, 85, 85, 85, 201, 201, 201, 201, 201, 201, 201, 201, 85, 85, 1, 1, 2, 2, 2, 1, 1, 6, 6, 35, 72, 201, 201, 201, 201, 85, 85, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 42, 24, 25, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 500
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040269 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040269
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040269/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040269
Building REAL300000040270
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040270'
/scratch/stefan/7769621/working/building/REAL300000040270 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040270

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040270/0 /scratch/stefan/7769621/working/building/REAL300000040270 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 363)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/363
`/scratch/stefan/7769621/working/3D/363' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C=C1)

`REAL300000040270.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040270.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040270/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040270 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', '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', '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, 1, 8, 8, 1, 11, 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]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 13, 15, 13, 15, 15, 13, 13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 13, 7, 1, 1, 1, 1, 1, 1, 1, 15, 15] 15
rigid atoms, others: [32, 33, 34, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 35, 22, 23, 24, 25, 26, 27, 36])
total number of confs: 43
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040270 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', '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', '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, 1, 8, 8, 1, 11, 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]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 5, 6, 15, 15, 15, 15, 15, 15, 15, 1, 1] 15
rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 22, 23, 24, 25, 36] 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: 31
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040270 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040270
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040270/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040270
Building REAL300000040271
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040271'
/scratch/stefan/7769621/working/building/REAL300000040271 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040271

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040271/0 /scratch/stefan/7769621/working/building/REAL300000040271 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 364)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/364
`/scratch/stefan/7769621/working/3D/364' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=CC=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1)

`REAL300000040271.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040271.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040271/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040271 none O=C([O-])COC1=CC=CC=C1C=NNC(=O)C1=CC2=CC=CC=C2C=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.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 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: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
145  conformations in input
total number of sets (complete confs): 145
using faster count positions algorithm for large data
unique positions, atoms: [145, 145, 145, 93, 33, 33, 33, 15, 33, 33, 15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 145, 145, 33, 33, 33, 33, 15, 7, 1, 1, 1, 1, 1, 1, 1] 145
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 14, 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, 15, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 482
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040271 none O=C([O-])COC1=CC=CC=C1C=NNC(=O)C1=CC2=CC=CC=C2C=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.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 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: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [61, 43, 61, 10, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 33, 33, 33, 33, 33, 33, 33, 33, 33, 43, 43, 1, 1, 1, 1, 4, 10, 33, 33, 33, 33, 33, 33, 33] 145
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 3, 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])
total number of confs: 255
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040271 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040271
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040271/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040271
Building REAL300000040272
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040272'
/scratch/stefan/7769621/working/building/REAL300000040272 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040272

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040272/0 /scratch/stefan/7769621/working/building/REAL300000040272 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 365)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/365
`/scratch/stefan/7769621/working/3D/365' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1)

`REAL300000040272.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040272.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040272/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040272 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=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.am', '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', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
111  conformations in input
total number of sets (complete confs): 111
using faster count positions algorithm for large data
unique positions, atoms: [15, 1, 15, 15, 34, 34, 41, 111, 111, 111, 111, 111, 111, 111, 111, 111, 1, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 13, 15, 15, 34, 111, 111, 111, 111, 111, 111, 111, 12, 12, 1, 1, 12, 12] 111
rigid atoms, others: [43, 44, 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, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46])
total number of confs: 242
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: REAL300000040272 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=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.am', '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', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
111  conformations in input
total number of sets (complete confs): 111
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 13, 13, 13, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 5, 5, 5, 13, 53, 53, 53, 53, 53, 53, 53, 1, 1, 12, 12, 1, 1] 111
rigid atoms, others: [1, 41, 42, 45, 46, 16, 17, 18, 19, 20, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44])
total number of confs: 99
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040272 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=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.am', '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', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
111  conformations in input
total number of sets (complete confs): 111
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 53, 53, 18, 29, 111, 111, 111, 111, 111, 111, 111, 53, 53, 15, 15, 15, 7, 1, 1, 1, 1, 1, 1, 1, 53, 53, 111, 111, 53, 53] 111
rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46])
total number of confs: 276
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040272 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040272
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040272/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040272
Building REAL300000040273
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040273'
/scratch/stefan/7769621/working/building/REAL300000040273 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040273

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040273/0 /scratch/stefan/7769621/working/building/REAL300000040273 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 366)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/366
`/scratch/stefan/7769621/working/3D/366' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=CC=C1OCC(=O)[O-])

`REAL300000040273.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040273.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040273/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040273 none COC1=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=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.am', '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', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 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, 6, 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]
0  hydrogens 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, 36, 36, 12, 12, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 133, 201, 201, 201, 60, 60, 60, 36, 12, 5, 1, 1, 1, 1, 1, 1, 1, 36, 36, 201, 201] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44])
total number of confs: 537
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040273 none COC1=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=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.am', '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', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 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, 6, 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]
0  hydrogens 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, 12, 12, 12, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 9, 33, 49, 49, 4, 4, 4, 1, 7, 12, 36, 36, 36, 36, 36, 36, 36, 1, 1, 33, 33] 201
rigid atoms, others: [1, 2, 3, 4, 5, 41, 42, 20, 21, 22, 23, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44])
total number of confs: 237
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040273 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040273
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040273/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040273
Building REAL300000040274
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040274'
/scratch/stefan/7769621/working/building/REAL300000040274 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040274

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040274/0 /scratch/stefan/7769621/working/building/REAL300000040274 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 367)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/367
`/scratch/stefan/7769621/working/3D/367' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C=C1)

`REAL300000040274.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040274.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040274/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040274 none O=C([O-])COC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=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.am', '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', 'C.ar', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 127, 77, 54, 80, 80, 31, 31, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 80, 80, 201, 201, 80, 80, 31, 7, 1, 1, 1, 1, 1, 1, 1, 80, 80] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40])
total number of confs: 675
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040274 none O=C([O-])COC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=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.am', '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', 'C.ar', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [33, 15, 33, 3, 1, 1, 1, 1, 1, 1, 8, 8, 31, 31, 31, 80, 80, 80, 80, 80, 80, 80, 80, 80, 1, 1, 16, 16, 1, 1, 8, 31, 80, 80, 80, 80, 80, 80, 80, 1, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 39, 40, 24, 25, 28, 29] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 256
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040274 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040274
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040274/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040274
Building REAL300000040275
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040275'
/scratch/stefan/7769621/working/building/REAL300000040275 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040275

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040275/0 /scratch/stefan/7769621/working/building/REAL300000040275 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 368)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/368
`/scratch/stefan/7769621/working/3D/368' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=CC(OCC(=O)[O-])=C1)

`REAL300000040275.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040275.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040275/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040275 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 19, 19, 19, 61, 61, 61, 61, 61, 61, 61, 61, 61, 1, 1, 1, 1, 1, 1, 6, 22, 32, 32, 1, 11, 11, 11, 19, 61, 61, 61, 61, 61, 61, 61, 1, 1, 1, 22, 22, 1] 201
rigid atoms, others: [1, 38, 39, 40, 43, 16, 17, 18, 19, 20, 21, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42])
total number of confs: 209
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040275 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 61, 61, 61, 61, 61, 123, 201, 201, 201, 61, 15, 15, 15, 7, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 201, 201, 61] 201
rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 36, 31] set([0, 1, 2, 3, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43])
total number of confs: 557
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040275 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040275
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040275/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040275
Building REAL300000040276
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040276'
/scratch/stefan/7769621/working/building/REAL300000040276 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040276

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040276/0 /scratch/stefan/7769621/working/building/REAL300000040276 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 369)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/369
`/scratch/stefan/7769621/working/3D/369' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1)

`REAL300000040276.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040276.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040276/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040276 none O=C([O-])C1=CC=CC=C1C=NNC(=O)C1=CC2=CC=CC=C2C=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.2', 'N.2', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 21, 21, 21, 11, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 11, 7, 1, 1, 1, 1, 1, 1, 1] 21
rigid atoms, others: [32, 33, 34, 35, 36, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 24, 25, 26, 27, 28, 29])
total number of confs: 39
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040276 none O=C([O-])C1=CC=CC=C1C=NNC(=O)C1=CC2=CC=CC=C2C=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.2', 'N.2', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 6, 12, 21, 21, 21, 21, 21, 21, 21] 21
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 27] set([0, 2, 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: 55
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040276 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040276
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040276/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040276
Building REAL300000040277
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040277'
/scratch/stefan/7769621/working/building/REAL300000040277 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040277

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040277/0 /scratch/stefan/7769621/working/building/REAL300000040277 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 370)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/370
`/scratch/stefan/7769621/working/3D/370' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=C(C(=O)[O-])C=C1)

`REAL300000040277.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040277.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040277/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040277 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 4, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1] 25
rigid atoms, others: [1, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 51
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040277 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 25, 25, 9, 25, 25, 25, 25, 25, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 25
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39])
total number of confs: 99
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040277 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040277
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040277/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040277
Building REAL300000040278
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040278'
/scratch/stefan/7769621/working/building/REAL300000040278 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040278

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040278/0 /scratch/stefan/7769621/working/building/REAL300000040278 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 371)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/371
`/scratch/stefan/7769621/working/3D/371' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=C(CC(=O)[O-])C=C1)

`REAL300000040278.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040278.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040278/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040278 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 4, 10, 10, 10, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 4, 4, 4, 10, 31, 31, 31, 31, 31, 31, 31, 1, 1, 2, 2, 1, 1] 55
rigid atoms, others: [1, 37, 38, 41, 42, 16, 17, 18, 19, 20, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40])
total number of confs: 75
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040278 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 31, 31, 11, 11, 55, 55, 55, 31, 31, 11, 11, 11, 7, 1, 1, 1, 1, 1, 1, 1, 31, 31, 55, 55, 31, 31] 55
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 36, 30, 31] set([0, 1, 2, 3, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42])
total number of confs: 255
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040278 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040278
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040278/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040278
Building REAL300000040279
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040279'
/scratch/stefan/7769621/working/building/REAL300000040279 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040279

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040279/0 /scratch/stefan/7769621/working/building/REAL300000040279 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 372)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/372
`/scratch/stefan/7769621/working/3D/372' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])OC2=C1C(=NNC(=O)C1=CC3=CC=CC=C3C=C1)CCC2)

`REAL300000040279.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040279.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040279/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040279 none CC1=C(C(=O)[O-])OC2=C1C(=NNC(=O)C1=CC3=CC=CC=C3C=C1)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.am', '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.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 7, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27] 27
rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43])
total number of confs: 39
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040279 none CC1=C(C(=O)[O-])OC2=C1C(=NNC(=O)C1=CC3=CC=CC=C3C=C1)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.am', '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.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 2, 2, 2, 8, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1] 27
rigid atoms, others: [0, 1, 2, 3, 38, 6, 7, 8, 9, 10, 11, 40, 43, 41, 24, 25, 26, 42, 39] set([4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 55
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040279 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040279
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040279/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040279
Building REAL300000040280
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040280'
/scratch/stefan/7769621/working/building/REAL300000040280 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040280

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040280/0 /scratch/stefan/7769621/working/building/REAL300000040280 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 373)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/373
`/scratch/stefan/7769621/working/3D/373' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C=C1)

`REAL300000040280.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040280.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040280/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040280 none O=C([O-])CCOC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', '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', '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, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 173, 118, 72, 48, 73, 73, 27, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 73, 73, 201, 201, 173, 173, 73, 73, 27, 7, 1, 1, 1, 1, 1, 1, 1, 73, 73] 201
rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43])
total number of confs: 686
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040280 none O=C([O-])CCOC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', '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', '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, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 29, 13, 3, 1, 1, 1, 1, 1, 1, 10, 10, 30, 30, 30, 73, 73, 73, 73, 73, 73, 73, 73, 73, 1, 1, 21, 21, 14, 14, 1, 1, 10, 30, 73, 73, 73, 73, 73, 73, 73, 1, 1] 201
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 43, 25, 26, 42, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 249
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040280 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040280
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040280/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040280
Building REAL300000040281
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040281'
/scratch/stefan/7769621/working/building/REAL300000040281 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040281

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040281/0 /scratch/stefan/7769621/working/building/REAL300000040281 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 374)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/374
`/scratch/stefan/7769621/working/3D/374' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=C1)C(=O)[O-])

`REAL300000040281.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040281.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040281/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040281 none CC(OC1=CC=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=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.am', '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', '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, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 159, 46, 46, 46, 46, 46, 21, 21, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 201, 201, 201, 201, 201, 201, 201, 46, 46, 46, 21, 6, 1, 1, 1, 1, 1, 1, 1, 46] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43])
total number of confs: 457
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040281 none CC(OC1=CC=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=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.am', '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', '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, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [31, 11, 1, 1, 1, 1, 1, 1, 1, 9, 9, 15, 15, 15, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 31, 42, 42, 31, 31, 31, 31, 1, 1, 1, 9, 15, 46, 46, 46, 46, 46, 46, 46, 1] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 43, 23, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 219
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040281 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040281
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040281/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040281
Building REAL300000040282
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040282'
/scratch/stefan/7769621/working/building/REAL300000040282 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040282

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040282/0 /scratch/stefan/7769621/working/building/REAL300000040282 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 375)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/375
`/scratch/stefan/7769621/working/3D/375' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=C1)

`REAL300000040282.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040282.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040282/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040282 none O=C([O-])CCOC1=CC=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', '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', '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, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 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: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 200, 177, 133, 46, 46, 46, 46, 46, 21, 21, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 201, 201, 177, 177, 46, 46, 46, 21, 5, 1, 1, 1, 1, 1, 1, 1, 46] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 14, 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, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43])
total number of confs: 526
number of broken/clashed sets: 24
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040282 none O=C([O-])CCOC1=CC=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', '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', '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, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 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: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 39, 22, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 15, 15, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 32, 32, 22, 22, 1, 1, 1, 6, 14, 46, 46, 46, 46, 46, 46, 46, 1] 201
rigid atoms, others: [32, 33, 43, 5, 6, 7, 8, 9, 10, 11, 26, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 250
number of broken/clashed sets: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040282 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040282
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040282/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040282
Building REAL300000040283
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040283'
/scratch/stefan/7769621/working/building/REAL300000040283 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040283

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040283/0 /scratch/stefan/7769621/working/building/REAL300000040283 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 376)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/376
`/scratch/stefan/7769621/working/3D/376' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C=C1[N+](=O)[O-])

`REAL300000040283.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040283.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040283/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040283 none O=C([O-])COC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)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', 'N.am', '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', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 165, 64, 38, 64, 64, 21, 21, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 64, 201, 201, 64, 64, 21, 5, 1, 1, 1, 1, 1, 1, 1, 64] 201
rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42])
total number of confs: 523
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040283 none O=C([O-])COC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)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', 'N.am', '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', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 27, 31, 7, 1, 1, 1, 1, 1, 1, 8, 8, 20, 20, 20, 64, 64, 64, 64, 64, 64, 64, 64, 64, 1, 1, 1, 2, 2, 27, 27, 1, 1, 8, 20, 64, 64, 64, 64, 64, 64, 64, 1] 201
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 42, 24, 25, 26, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 216
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040283 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040283
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040283/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040283
Building REAL300000040284
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040284'
/scratch/stefan/7769621/working/building/REAL300000040284 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040284

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040284/0 /scratch/stefan/7769621/working/building/REAL300000040284 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 377)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/377
`/scratch/stefan/7769621/working/3D/377' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=C1)

`REAL300000040284.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040284.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040284/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040284 none O=C([O-])COC1=CC=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=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', 'N.am', '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', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 138, 49, 49, 49, 49, 49, 27, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 201, 201, 49, 49, 49, 27, 7, 1, 1, 1, 1, 1, 1, 1, 49] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 25, 26, 27, 28, 29, 30, 31, 32, 40])
total number of confs: 526
number of broken/clashed sets: 35
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040284 none O=C([O-])COC1=CC=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=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', 'N.am', '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', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 46, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 15, 16, 16, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 28, 28, 1, 1, 1, 7, 15, 49, 49, 49, 49, 49, 49, 49, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 40, 25, 28, 29, 30] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 231
number of broken/clashed sets: 35
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040284 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040284
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040284/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040284
Building REAL300000040285
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040285'
/scratch/stefan/7769621/working/building/REAL300000040285 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040285

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040285/0 /scratch/stefan/7769621/working/building/REAL300000040285 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 378)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/378
`/scratch/stefan/7769621/working/3D/378' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C(OCC(=O)[O-])=C1)

`REAL300000040285.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040285.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040285/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040285 none COC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)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.am', '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', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 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, 4, 7, 6, 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]
0  hydrogens 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, 37, 15, 37, 37, 15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 113, 201, 201, 201, 37, 61, 61, 61, 37, 37, 15, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 37] 201
rigid atoms, others: [35, 36, 37, 38, 39, 40, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44])
total number of confs: 685
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040285 none COC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)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.am', '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', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 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, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 9, 43, 63, 63, 1, 3, 3, 3, 1, 1, 6, 12, 37, 37, 37, 37, 37, 37, 37, 43, 43, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 44, 21, 22, 27, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 278
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040285 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040285
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040285/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040285
Building REAL300000040286
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040286'
/scratch/stefan/7769621/working/building/REAL300000040286 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040286

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040286/0 /scratch/stefan/7769621/working/building/REAL300000040286 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 379)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/379
`/scratch/stefan/7769621/working/3D/379' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C(F)(F)OC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C=C1)

`REAL300000040286.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040286.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040286/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040286 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 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]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 130, 201, 201, 61, 38, 61, 61, 21, 21, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 21, 5, 1, 1, 1, 1, 1, 1, 1, 61, 61] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 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, 15, 26, 27, 28, 29, 30, 31, 39, 40])
total number of confs: 611
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040286 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 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]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 38, 7, 28, 28, 1, 1, 1, 1, 1, 1, 8, 8, 18, 19, 18, 61, 61, 61, 61, 61, 61, 61, 61, 61, 1, 1, 1, 1, 8, 18, 61, 61, 61, 61, 61, 61, 61, 1, 1] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 40, 39, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 236
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040286 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040286
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040286/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040286
Building REAL300000040287
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040287'
/scratch/stefan/7769621/working/building/REAL300000040287 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040287

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040287/0 /scratch/stefan/7769621/working/building/REAL300000040287 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 380)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/380
`/scratch/stefan/7769621/working/3D/380' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C=C1)

`REAL300000040287.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040287.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040287/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040287 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)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.am', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 19, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 19, 7, 1, 1, 1, 1, 1, 1, 1, 27, 27] 27
rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 15, 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, 16, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43])
total number of confs: 43
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040287 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)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.am', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 6, 6, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 3, 3, 3, 1, 6, 10, 27, 27, 27, 27, 27, 27, 27, 1, 1] 27
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 43, 27, 28, 42] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 60
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040287 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040287
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040287/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040287
Building REAL300000040288
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040288'
/scratch/stefan/7769621/working/building/REAL300000040288 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040288

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040288/0 /scratch/stefan/7769621/working/building/REAL300000040288 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 381)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/381
`/scratch/stefan/7769621/working/3D/381' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)N1)

`REAL300000040288.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040288.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040288/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040288 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [35, 35, 35, 35, 35, 35, 17, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 17, 7, 1, 1, 1, 1, 1, 1, 1, 35] 35
rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 34, 22, 23, 24, 25, 26])
total number of confs: 61
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040288 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 13, 13, 13, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 8, 13, 35, 35, 35, 35, 35, 35, 35, 1] 35
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 22, 23, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 60
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040288 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040288
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040288/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040288
Building REAL300000040289
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040289'
/scratch/stefan/7769621/working/building/REAL300000040289 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040289

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040289/0 /scratch/stefan/7769621/working/building/REAL300000040289 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 382)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/382
`/scratch/stefan/7769621/working/3D/382' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=C(C(=O)[O-])C=C1)

`REAL300000040289.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040289.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040289/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040289 none CCC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 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: [15, 6, 1, 6, 6, 23, 23, 23, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 23, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1] 52
rigid atoms, others: [2, 39, 40, 41, 42, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 140
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040289 none CCC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 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: [33, 24, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 45, 45, 25, 39, 45, 45, 45, 45, 33, 33, 33, 33, 33, 7, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45] 52
rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 37] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42])
total number of confs: 204
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040289 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040289
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040289/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040289
Building REAL300000040290
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040290'
/scratch/stefan/7769621/working/building/REAL300000040290 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040290

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040290/0 /scratch/stefan/7769621/working/building/REAL300000040290 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 383)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/383
`/scratch/stefan/7769621/working/3D/383' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=CC=C1C(=O)[O-])

`REAL300000040290.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040290.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040290/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040290 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 5, 9, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 9, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1] 25
rigid atoms, others: [1, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22] set([0, 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])
total number of confs: 53
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040290 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 25, 25, 25, 25, 25, 25, 25, 25, 13, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 25
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39])
total number of confs: 39
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040290 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040290
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040290/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040290
Building REAL300000040291
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040291'
/scratch/stefan/7769621/working/building/REAL300000040291 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040291

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040291/0 /scratch/stefan/7769621/working/building/REAL300000040291 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 384)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/384
`/scratch/stefan/7769621/working/3D/384' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC(C(=O)[O-])=CC=C1O)

`REAL300000040291.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040291.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040291/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040291 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 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]
1  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 7, 15, 15, 15, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 2] 78
rigid atoms, others: [1, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 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, 40])
total number of confs: 81
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040291 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 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]
1  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: [19, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 39, 39, 39, 39, 39, 39, 39, 39, 39, 19, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 78] 78
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 36, 30, 31] set([0, 1, 2, 3, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40])
total number of confs: 139
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040291 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040291
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040291/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040291
Building REAL300000040292
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040292'
/scratch/stefan/7769621/working/building/REAL300000040292 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040292

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040292/0 /scratch/stefan/7769621/working/building/REAL300000040292 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 385)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/385
`/scratch/stefan/7769621/working/3D/385' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC(C(=O)[O-])=CC=C1F)

`REAL300000040292.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040292.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040292/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040292 none CCC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 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, 6, 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
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [34, 12, 1, 12, 12, 40, 40, 40, 105, 105, 105, 105, 105, 105, 105, 105, 105, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 34, 34, 34, 34, 34, 40, 105, 105, 105, 105, 105, 105, 105, 1, 1, 1] 115
rigid atoms, others: [2, 40, 41, 42, 17, 18, 19, 20, 23, 24, 25, 26] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 309
number of broken/clashed sets: 53
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040292 none CCC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 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, 6, 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
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [61, 27, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 105, 105, 105, 105, 105, 105, 105, 105, 105, 61, 61, 61, 61, 61, 7, 1, 1, 1, 1, 1, 1, 1, 105, 105, 105] 115
rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 39, 37] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42])
total number of confs: 305
number of broken/clashed sets: 53
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040292 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040292
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040292/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040292
Building REAL300000040293
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040293'
/scratch/stefan/7769621/working/building/REAL300000040293 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040293

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040293/0 /scratch/stefan/7769621/working/building/REAL300000040293 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 386)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/386
`/scratch/stefan/7769621/working/3D/386' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=NNC(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)=C2C=C1)

`REAL300000040293.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040293.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040293/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040293 none O=C([O-])C1=CC2=NNC(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', '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', 'C.ar', '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, 8, 8, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 15, 7, 1, 1, 1, 1, 1, 1, 1, 19, 19] 19
rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 24, 25, 26, 27, 28, 29, 30, 38, 39])
total number of confs: 35
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040293 none O=C([O-])C1=CC2=NNC(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', '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', 'C.ar', '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, 8, 8, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 4, 6, 19, 19, 19, 19, 19, 19, 19, 1, 1] 19
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 38, 24, 25, 26, 27, 28] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 33
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040293 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040293/1 /scratch/stefan/7769621/working/building/REAL300000040293 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 387)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/387
`/scratch/stefan/7769621/working/3D/387' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)=NNC2=C1)

`REAL300000040293.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040293.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040293/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040293 none O=C([O-])C1=CC=C2C(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)=NNC2=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', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', '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, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 17, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 17, 7, 1, 1, 1, 1, 1, 1, 1, 42, 42] 42
rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39])
total number of confs: 68
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040293 none O=C([O-])C1=CC=C2C(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)=NNC2=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', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', '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, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 13, 13, 13, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 1, 1, 8, 13, 42, 42, 42, 42, 42, 42, 42, 1, 1] 42
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 38, 39, 23, 24, 25, 26, 27, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 78
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040293 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040293
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040293/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040293/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040293
Building REAL300000040294
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040294'
/scratch/stefan/7769621/working/building/REAL300000040294 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040294

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040294/0 /scratch/stefan/7769621/working/building/REAL300000040294 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 388)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/388
`/scratch/stefan/7769621/working/3D/388' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=CC(C(=O)[O-])=C1)

`REAL300000040294.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040294.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040294/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040294 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [11, 1, 11, 11, 15, 15, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 11, 11, 15, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1] 33
rigid atoms, others: [1, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 71
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040294 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 15, 7, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33] 33
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39])
total number of confs: 53
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040294 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040294
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040294/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040294
Building REAL300000040295
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040295'
/scratch/stefan/7769621/working/building/REAL300000040295 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040295

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040295/0 /scratch/stefan/7769621/working/building/REAL300000040295 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 389)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/389
`/scratch/stefan/7769621/working/3D/389' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CN1C=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)N=N1)

`REAL300000040295.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040295.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040295/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040295 none O=C([O-])CN1C=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
104  conformations in input
total number of sets (complete confs): 104
using faster count positions algorithm for large data
unique positions, atoms: [104, 104, 104, 69, 69, 69, 31, 31, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69, 104, 104, 69, 31, 7, 1, 1, 1, 1, 1, 1, 1] 104
rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 254
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040295 none O=C([O-])CN1C=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
104  conformations in input
total number of sets (complete confs): 104
using faster count positions algorithm for large data
unique positions, atoms: [15, 8, 15, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 69, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1, 8, 8, 1, 7, 21, 69, 69, 69, 69, 69, 69, 69] 104
rigid atoms, others: [3, 4, 5, 6, 7, 22, 23, 26] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 163
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040295 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040295
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040295/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040295
Building REAL300000040296
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040296'
/scratch/stefan/7769621/working/building/REAL300000040296 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040296

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040296/0 /scratch/stefan/7769621/working/building/REAL300000040296 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 390)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/390
`/scratch/stefan/7769621/working/3D/390' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=C(C(=O)[O-])C(F)=C1)

`REAL300000040296.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040296.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040296/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040296 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 22, 22, 22, 73, 73, 73, 73, 73, 73, 73, 73, 73, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 11, 11, 11, 22, 73, 73, 73, 73, 73, 73, 73, 1, 1, 1] 73
rigid atoms, others: [1, 37, 38, 39, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 135
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040296 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 73, 73, 73, 73, 73, 73, 73, 73, 73, 19, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 73, 73, 73] 73
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 36, 30, 31] set([0, 1, 2, 3, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39])
total number of confs: 103
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040296 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040296
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040296/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040296
Building REAL300000040297
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040297'
/scratch/stefan/7769621/working/building/REAL300000040297 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040297

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040297/0 /scratch/stefan/7769621/working/building/REAL300000040297 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 391)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/391
`/scratch/stefan/7769621/working/3D/391' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CSC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=C1)

`REAL300000040297.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040297.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040297/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040297 none O=C([O-])C1=CSC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [35, 35, 35, 35, 35, 35, 19, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 19, 7, 1, 1, 1, 1, 1, 1, 1, 35] 35
rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 33])
total number of confs: 59
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040297 none O=C([O-])C1=CSC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 16, 16, 16, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 9, 16, 35, 35, 35, 35, 35, 35, 35, 1] 35
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 33] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 68
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040297 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040297
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040297/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040297
Building REAL300000040298
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040298'
/scratch/stefan/7769621/working/building/REAL300000040298 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040298

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040298/0 /scratch/stefan/7769621/working/building/REAL300000040298 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 392)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/392
`/scratch/stefan/7769621/working/3D/392' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=CC=C1OCCC(=O)[O-])

`REAL300000040298.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040298.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040298/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040298 none COC1=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=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.am', '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', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 25, 25, 25, 6, 6, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 103, 174, 178, 201, 181, 47, 47, 47, 25, 6, 5, 1, 1, 1, 1, 1, 1, 1, 25, 25, 174, 174, 178, 178] 201
rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47])
total number of confs: 638
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040298 none COC1=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=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.am', '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', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 9, 28, 32, 46, 40, 4, 4, 4, 1, 7, 8, 25, 25, 25, 25, 25, 25, 25, 1, 1, 28, 28, 31, 31] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 42, 43, 20, 21, 22, 23] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47])
total number of confs: 213
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040298 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040298
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040298/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040298
Building REAL300000040299
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040299'
/scratch/stefan/7769621/working/building/REAL300000040299 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040299

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040299/0 /scratch/stefan/7769621/working/building/REAL300000040299 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 393)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/393
`/scratch/stefan/7769621/working/3D/393' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C(Cl)=C1)

`REAL300000040299.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040299.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040299/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040299 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', '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', 'Cl', 'C.ar', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [27, 27, 27, 27, 27, 27, 17, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 17, 5, 1, 1, 1, 1, 1, 1, 1, 27] 27
rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28, 36])
total number of confs: 47
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040299 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', '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', 'Cl', 'C.ar', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 16, 16, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 10, 16, 27, 27, 27, 27, 27, 27, 27, 1] 27
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 36] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 63
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040299 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040299
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040299/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040299
Building REAL300000040300
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040300'
/scratch/stefan/7769621/working/building/REAL300000040300 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040300

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040300/0 /scratch/stefan/7769621/working/building/REAL300000040300 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 394)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/394
`/scratch/stefan/7769621/working/3D/394' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC(C(=O)[O-])=C(C)N=C1C)

`REAL300000040300.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040300.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040300/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040300 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC(C(=O)[O-])=C(C)N=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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]
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, 25, 25, 25, 65, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 9, 9, 9, 25, 65, 65, 65, 65, 65, 65, 65, 1, 2, 2, 2, 2, 2, 2] 65
rigid atoms, others: [1, 38, 16, 17, 18, 19, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44])
total number of confs: 149
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040300 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC(C(=O)[O-])=C(C)N=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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]
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: [19, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 19, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 65, 65] 65
rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 36, 31] set([0, 1, 2, 3, 5, 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: 91
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040300 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040300
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040300/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040300
Building REAL300000040301
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040301'
/scratch/stefan/7769621/working/building/REAL300000040301 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040301

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040301/0 /scratch/stefan/7769621/working/building/REAL300000040301 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 395)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/395
`/scratch/stefan/7769621/working/3D/395' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=CC=C1O)

`REAL300000040301.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040301.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040301/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040301 none O=C([O-])C1=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.ar', 'O.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, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [32, 32, 32, 32, 32, 17, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 17, 5, 1, 1, 1, 1, 1, 1, 1, 32, 32, 64] 64
rigid atoms, others: [32, 33, 34, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 35, 21, 22, 23, 24, 25, 26, 27, 37, 36])
total number of confs: 112
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040301 none O=C([O-])C1=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.ar', 'O.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, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 6, 6, 11, 11, 11, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 6, 11, 32, 32, 32, 32, 32, 32, 32, 1, 1, 2] 64
rigid atoms, others: [1, 3, 4, 5, 6, 35, 21, 22, 23, 24, 25, 36] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37])
total number of confs: 69
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040301 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040301
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040301/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040301
Building REAL300000040302
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040302'
/scratch/stefan/7769621/working/building/REAL300000040302 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040302

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040302/0 /scratch/stefan/7769621/working/building/REAL300000040302 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 396)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/396
`/scratch/stefan/7769621/working/3D/396' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC(C(=O)[O-])=CC=C1C)

`REAL300000040302.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040302.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040302/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040302 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.ar', '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, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [9, 1, 9, 9, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 12, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 2, 2, 2] 30
rigid atoms, others: [1, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 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, 40, 41, 42])
total number of confs: 64
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040302 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.ar', '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, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [16, 16, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 30, 30, 30, 30, 30, 30, 30, 30, 30, 16, 16, 16, 7, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30] 30
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 36, 30, 31] set([0, 1, 2, 3, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42])
total number of confs: 53
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040302 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040302
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040302/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040302
Building REAL300000040303
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040303'
/scratch/stefan/7769621/working/building/REAL300000040303 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040303

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040303/0 /scratch/stefan/7769621/working/building/REAL300000040303 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 397)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/397
`/scratch/stefan/7769621/working/3D/397' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=C(C(=O)[O-])O1)

`REAL300000040303.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040303.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040303/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040303 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [6, 1, 6, 6, 6, 6, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 1, 1] 15
rigid atoms, others: [1, 35, 36, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 29
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040303 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [11, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 15, 15, 15, 15, 15, 15, 15, 11, 11, 11, 7, 1, 1, 1, 1, 1, 1, 1, 15, 15] 15
rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 36, 5, 35, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 31
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040303 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040303
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040303/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040303
Building REAL300000040304
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040304'
/scratch/stefan/7769621/working/building/REAL300000040304 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040304

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040304/0 /scratch/stefan/7769621/working/building/REAL300000040304 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 398)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/398
`/scratch/stefan/7769621/working/3D/398' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C=C1)C(=O)[O-])

`REAL300000040304.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040304.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040304/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040304 none CC(OC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)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.am', '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', '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, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 70, 56, 88, 88, 33, 33, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 88, 88, 201, 201, 201, 201, 201, 201, 201, 88, 88, 33, 7, 1, 1, 1, 1, 1, 1, 1, 88, 88] 201
rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43])
total number of confs: 565
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040304 none CC(OC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)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.am', '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', '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, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 1, 1, 1, 1, 1, 9, 9, 27, 27, 27, 88, 88, 88, 88, 88, 88, 88, 88, 88, 1, 1, 17, 24, 24, 17, 17, 17, 17, 1, 1, 9, 27, 88, 88, 88, 88, 88, 88, 88, 1, 1] 201
rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 42, 43, 22, 23, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 232
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040304 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040304
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040304/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040304
Building REAL300000040305
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040305'
/scratch/stefan/7769621/working/building/REAL300000040305 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040305

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040305/0 /scratch/stefan/7769621/working/building/REAL300000040305 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 399)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/399
`/scratch/stefan/7769621/working/3D/399' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1CCC(=NNC(=O)C2=CC3=CC=CC=C3C=C2)C2=CC=CC=C21)

`REAL300000040305.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040305.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040305/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040305 none O=C([O-])C1CCC(=NNC(=O)C2=CC3=CC=CC=C3C=C2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', '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', '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: [11, 1, 11, 5, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 11
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43])
total number of confs: 21
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040305 none O=C([O-])C1CCC(=NNC(=O)C2=CC3=CC=CC=C3C=C2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', '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', '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: [11, 1, 11, 5, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1] 11
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42, 43] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 25
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040305 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040305
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040305/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040305
Building REAL300000040306
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040306'
/scratch/stefan/7769621/working/building/REAL300000040306 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040306

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040306/0 /scratch/stefan/7769621/working/building/REAL300000040306 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 400)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/400
`/scratch/stefan/7769621/working/3D/400' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CN1C=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C2=CC=CC=C21)

`REAL300000040306.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040306.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040306/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040306 none O=C([O-])CN1C=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', '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', '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: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 159, 159, 82, 82, 82, 27, 27, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 82, 82, 159, 159, 82, 27, 5, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82] 159
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43])
total number of confs: 503
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040306 none O=C([O-])CN1C=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', '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', '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: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 7, 13, 1, 1, 1, 1, 1, 8, 8, 30, 30, 30, 82, 82, 82, 82, 82, 82, 82, 82, 82, 1, 1, 1, 1, 1, 1, 7, 7, 1, 8, 30, 82, 82, 82, 82, 82, 82, 82, 1, 1, 1, 1] 159
rigid atoms, others: [3, 4, 5, 6, 7, 40, 41, 42, 43, 22, 23, 24, 25, 26, 27, 30] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 188
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040306 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040306
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040306/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040306
Building REAL300000040307
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040307'
/scratch/stefan/7769621/working/building/REAL300000040307 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040307

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040307/0 /scratch/stefan/7769621/working/building/REAL300000040307 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 401)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/401
`/scratch/stefan/7769621/working/3D/401' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])C=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)N1)

`REAL300000040307.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040307.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040307/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040307 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 23, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 23, 7, 1, 1, 1, 1, 1, 1, 1, 27] 27
rigid atoms, others: [32, 33, 34, 35, 36, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 23, 24, 25, 26, 27, 28, 29, 37])
total number of confs: 43
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040307 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 4, 4, 7, 7, 7, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 2, 2, 2, 1, 4, 6, 27, 27, 27, 27, 27, 27, 27, 1] 27
rigid atoms, others: [0, 1, 2, 3, 37, 6, 7, 8, 23, 27] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 55
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040307 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040307
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040307/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040307
Building REAL300000040308
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040308'
/scratch/stefan/7769621/working/building/REAL300000040308 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040308

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040308/0 /scratch/stefan/7769621/working/building/REAL300000040308 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 402)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/402
`/scratch/stefan/7769621/working/3D/402' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=C1)

`REAL300000040308.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040308.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040308/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040308 none O=C([O-])C1=CC=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=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.2', 'N.2', 'N.am', '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', '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, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 21, 21, 13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 13, 5, 1, 1, 1, 1, 1, 1, 1, 21] 21
rigid atoms, others: [32, 33, 34, 35, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 23, 24, 25, 26, 27, 28, 36])
total number of confs: 35
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040308 none O=C([O-])C1=CC=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=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.2', 'N.2', 'N.am', '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', '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, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 9, 9, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 7, 9, 21, 21, 21, 21, 21, 21, 21, 1] 21
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 36] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 41
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040308 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040308
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040308/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040308
Building REAL300000040309
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040309'
/scratch/stefan/7769621/working/building/REAL300000040309 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040309

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040309/0 /scratch/stefan/7769621/working/building/REAL300000040309 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 403)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/403
`/scratch/stefan/7769621/working/3D/403' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=CC(OCCCC(=O)[O-])=C1)

`REAL300000040309.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040309.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040309/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040309 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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]
0  hydrogens 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, 9, 9, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 5, 15, 25, 37, 39, 39, 1, 9, 9, 9, 9, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 15, 15, 25, 25, 37, 37, 1] 201
rigid atoms, others: [1, 49, 40, 41, 42, 16, 17, 18, 19, 20, 21, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47, 48])
total number of confs: 205
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040309 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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]
0  hydrogens 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, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 28, 28, 28, 28, 28, 60, 132, 159, 201, 201, 201, 28, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 132, 132, 159, 159, 201, 201, 28] 201
rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 36, 38, 39] set([0, 1, 2, 3, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 788
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040309 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040309
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040309/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040309
Building REAL300000040310
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040310'
/scratch/stefan/7769621/working/building/REAL300000040310 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040310

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040310/0 /scratch/stefan/7769621/working/building/REAL300000040310 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 404)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/404
`/scratch/stefan/7769621/working/3D/404' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CC=C(OCC(=O)[O-])C=C1)=NNC(=O)C1=CC2=CC=CC=C2C=C1)

`REAL300000040310.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040310.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040310/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040310 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)=NNC(=O)C1=CC2=CC=CC=C2C=C1 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', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 46, 50, 50, 50, 50, 50, 139, 201, 201, 201, 50, 50, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 46, 46, 50, 50, 50, 50, 201, 201, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [49, 43, 44, 45, 46, 47, 48, 17, 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, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 601
number of broken/clashed sets: 187
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040310 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)=NNC(=O)C1=CC2=CC=CC=C2C=C1 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', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 4, 2, 1, 1, 1, 1, 1, 1, 6, 17, 28, 28, 1, 1, 7, 7, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 4, 4, 2, 2, 1, 1, 17, 17, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50] 201
rigid atoms, others: [3, 36, 5, 6, 7, 8, 41, 13, 14, 40, 4, 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, 32, 33, 34, 35, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 189
number of broken/clashed sets: 187
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040310 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040310
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040310/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040310
Building REAL300000040311
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040311'
/scratch/stefan/7769621/working/building/REAL300000040311 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040311

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040311/0 /scratch/stefan/7769621/working/building/REAL300000040311 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 405)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/405
`/scratch/stefan/7769621/working/3D/405' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1)

`REAL300000040311.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040311.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040311/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040311 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 18, 18, 18, 61, 61, 61, 61, 61, 61, 61, 61, 61, 1, 1, 1, 1, 1, 1, 11, 27, 27, 38, 38, 1, 11, 11, 11, 18, 61, 61, 61, 61, 61, 61, 61, 1, 1, 1, 27, 27, 27, 27, 1] 201
rigid atoms, others: [1, 39, 40, 41, 46, 16, 17, 18, 19, 20, 21, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45])
total number of confs: 225
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040311 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 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]
0  hydrogens 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, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 61, 61, 61, 61, 61, 162, 201, 201, 201, 201, 61, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 201, 201, 201, 201, 61] 201
rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 36, 38] set([0, 1, 2, 3, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 456
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040311 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040311
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040311/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040311
Building REAL300000040312
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040312'
/scratch/stefan/7769621/working/building/REAL300000040312 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040312

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040312/0 /scratch/stefan/7769621/working/building/REAL300000040312 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 406)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/406
`/scratch/stefan/7769621/working/3D/406' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CSC(C(=O)[O-])=C1)

`REAL300000040312.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040312.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040312/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040312 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 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, 6, 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
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [9, 1, 9, 9, 13, 13, 13, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 2, 2, 1, 9, 9, 9, 13, 37, 37, 37, 37, 37, 37, 37, 1, 1] 37
rigid atoms, others: [1, 35, 36, 16, 17, 18, 19, 20, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 75
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040312 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 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, 6, 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
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 37, 37, 37, 37, 37, 37, 37, 15, 15, 15, 7, 1, 1, 1, 1, 1, 1, 1, 37, 37] 37
rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 36, 5, 35, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 59
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040312 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040312
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040312/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040312
Building REAL300000040313
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040313'
/scratch/stefan/7769621/working/building/REAL300000040313 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040313

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040313/0 /scratch/stefan/7769621/working/building/REAL300000040313 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 407)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/407
`/scratch/stefan/7769621/working/3D/407' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1(C2=CC=CC=C2)CC(=NNC(=O)C2=CC3=CC=CC=C3C=C2)C1)

`REAL300000040313.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040313.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040313/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040313 none O=C([O-])C1(C2=CC=CC=C2)CC(=NNC(=O)C2=CC3=CC=CC=C3C=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.3', 'C.2', 'N.2', 'N.am', '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.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, 1, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [29, 21, 29, 21, 21, 29, 29, 21, 29, 29, 21, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 29, 29, 21, 29, 29, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 21, 21] 29
rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 14, 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, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43])
total number of confs: 105
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: REAL300000040313 none O=C([O-])C1(C2=CC=CC=C2)CC(=NNC(=O)C2=CC3=CC=CC=C3C=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.3', 'C.2', 'N.2', 'N.am', '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.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, 1, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [5, 4, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 1, 1, 1, 1, 1, 4, 4, 9, 29, 29, 29, 29, 29, 29, 29, 4, 4] 29
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27, 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, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 55
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040313 none O=C([O-])C1(C2=CC=CC=C2)CC(=NNC(=O)C2=CC3=CC=CC=C3C=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.3', 'C.2', 'N.2', 'N.am', '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.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, 1, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 4, 4, 1, 4, 4, 1, 1, 1, 1, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 4, 4, 1, 4, 4, 1, 1, 6, 21, 21, 21, 21, 21, 21, 21, 1, 1] 29
rigid atoms, others: [32, 1, 3, 4, 33, 10, 11, 12, 13, 43, 42, 26] set([0, 2, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 48
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040313 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040313
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040313/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040313
Building REAL300000040314
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040314'
/scratch/stefan/7769621/working/building/REAL300000040314 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040314

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040314/0 /scratch/stefan/7769621/working/building/REAL300000040314 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 408)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/408
`/scratch/stefan/7769621/working/3D/408' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C)

`REAL300000040314.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040314.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040314/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040314 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', '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, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 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, 6, 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]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 15, 15, 15, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 6, 10, 10, 1, 1, 1, 6, 6, 6, 15, 40, 40, 40, 40, 40, 40, 40, 1, 1, 6, 6, 2, 2, 2, 2, 2, 2] 54
rigid atoms, others: [1, 39, 40, 16, 17, 18, 19, 20, 21, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 116
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040314 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', '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, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 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, 6, 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]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 40, 40, 40, 40, 40, 54, 54, 54, 40, 40, 40, 19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 40, 40, 54, 54, 40, 40, 40, 40, 40, 40] 54
rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 36, 38] set([0, 1, 2, 3, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 184
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040314 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040314
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040314/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040314
Building REAL300000040315
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040315'
/scratch/stefan/7769621/working/building/REAL300000040315 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040315

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040315/0 /scratch/stefan/7769621/working/building/REAL300000040315 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 409)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/409
`/scratch/stefan/7769621/working/3D/409' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCCCCCC(=O)[O-])=NNC(=O)C1=CC2=CC=CC=C2C=C1)

`REAL300000040315.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040315.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040315/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040315 none CC(CCCCCCC(=O)[O-])=NNC(=O)C1=CC2=CC=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 5, 5, 5, 5, 1, 11, 11, 8, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 60, 64, 100, 120, 147, 201, 201, 201, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 60, 60, 76, 76, 94, 94, 136, 136, 158, 157, 197, 197, 5, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [45, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 1147
number of broken/clashed sets: 182
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040315 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040315
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040315/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040315
Building REAL300000040316
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040316'
/scratch/stefan/7769621/working/building/REAL300000040316 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040316

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040316/0 /scratch/stefan/7769621/working/building/REAL300000040316 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 410)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/410
`/scratch/stefan/7769621/working/3D/410' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(=NNC(=O)C2=CC3=CC=CC=C3C=C2)CCC1CC(=O)[O-])

`REAL300000040316.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040316.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040316/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040316 none CC1C(=NNC(=O)C2=CC3=CC=CC=C3C=C2)CCC1CC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', '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.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']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 11, 11, 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, 6, 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
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [24, 24, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 36, 36, 36, 24, 24, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 36, 36] 36
rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 91
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040316 none CC1C(=NNC(=O)C2=CC3=CC=CC=C3C=C2)CCC1CC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', '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.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']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 11, 11, 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, 6, 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
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 7, 11, 11, 2, 2, 2, 1, 8, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 7, 7] 36
rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 39, 40, 17, 18, 19, 20, 36, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42])
total number of confs: 80
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040316 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040316
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040316/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040316
Building REAL300000040317
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040317'
/scratch/stefan/7769621/working/building/REAL300000040317 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040317

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040317/0 /scratch/stefan/7769621/working/building/REAL300000040317 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 411)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/411
`/scratch/stefan/7769621/working/3D/411' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC(C(=O)[O-])=CS1)

`REAL300000040317.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040317.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040317/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040317 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [10, 1, 10, 10, 19, 19, 18, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 18, 41, 41, 41, 41, 41, 41, 41, 1, 1] 41
rigid atoms, others: [1, 35, 36, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 97
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040317 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [21, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 41, 41, 41, 41, 41, 41, 41, 21, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 41, 41] 41
rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 36, 5, 35, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 61
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040317 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040317
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040317/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040317
Building REAL300000040318
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040318'
/scratch/stefan/7769621/working/building/REAL300000040318 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040318

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040318/0 /scratch/stefan/7769621/working/building/REAL300000040318 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 412)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/412
`/scratch/stefan/7769621/working/3D/412' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(=NNC(=O)C2=CC3=CC=CC=C3C=C2)CCC(C(=O)[O-])C1(C)C)

`REAL300000040318.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040318.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040318/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040318 none CC1C(=NNC(=O)C2=CC3=CC=CC=C3C=C2)CCC(C(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', '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, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 11, 5, 5, 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, 7, 7, 7, 4, 7, 6, 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]
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, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 11
rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 37, 31] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 21
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040318 none CC1C(=NNC(=O)C2=CC3=CC=CC=C3C=C2)CCC(C(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', '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, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 11, 5, 5, 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, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 2, 1, 5, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 11
rigid atoms, others: [0, 1, 2, 3, 4, 38, 39, 40, 41, 42, 17, 18, 19, 20, 23, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48])
total number of confs: 43
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040318 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040318
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040318/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040318
Building REAL300000040319
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040319'
/scratch/stefan/7769621/working/building/REAL300000040319 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040319

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040319/0 /scratch/stefan/7769621/working/building/REAL300000040319 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 413)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/413
`/scratch/stefan/7769621/working/3D/413' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(C(=O)[O-])CCC1=NNC(=O)C1=CC2=CC=CC=C2C=C1)

`REAL300000040319.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040319.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040319/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040319 none CC1CC(C(=O)[O-])CCC1=NNC(=O)C1=CC2=CC=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 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, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 7, 1, 1, 1, 1, 1, 1, 1] 22
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 35
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040319 none CC1CC(C(=O)[O-])CCC1=NNC(=O)C1=CC2=CC=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 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, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 22, 22, 22, 22, 22, 22, 22] 22
rigid atoms, others: [0, 1, 2, 3, 4, 33, 7, 8, 9, 10, 11, 34, 32, 27, 28, 29, 30, 31] set([5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 50
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040319 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040319
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040319/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040319
Building REAL300000040320
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040320'
/scratch/stefan/7769621/working/building/REAL300000040320 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040320

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040320/0 /scratch/stefan/7769621/working/building/REAL300000040320 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 414)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/414
`/scratch/stefan/7769621/working/3D/414' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(=NNC(=O)C2=CC3=CC=CC=C3C=C2)CCC1C(=O)[O-])

`REAL300000040320.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040320.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040320/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040320 none CC1CC(=NNC(=O)C2=CC3=CC=CC=C3C=C2)CCC1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', '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.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, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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
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, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19] 19
rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42])
total number of confs: 31
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040320 none CC1CC(=NNC(=O)C2=CC3=CC=CC=C3C=C2)CCC1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', '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.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, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 1, 7, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1] 19
rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 39, 40, 41, 42, 18, 19, 20, 21, 27, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 45
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040320 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040320
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040320/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040320
Building REAL300000040321
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040321'
/scratch/stefan/7769621/working/building/REAL300000040321 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040321

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040321/0 /scratch/stefan/7769621/working/building/REAL300000040321 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 415)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/415
`/scratch/stefan/7769621/working/3D/415' -> `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(=NNC(=O)C2=CC3=CC=CC=C3C=C2)C1)

`REAL300000040321.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040321.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040321/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040321 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(=NNC(=O)C2=CC3=CC=CC=C3C=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', 'Cl', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.am', '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.3', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 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
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [35, 24, 35, 24, 24, 61, 61, 54, 61, 61, 61, 24, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 61, 61, 61, 61, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 24, 24] 61
rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 15, 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, 16, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43])
total number of confs: 170
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: REAL300000040321 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(=NNC(=O)C2=CC3=CC=CC=C3C=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', 'Cl', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.am', '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.3', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 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
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [13, 9, 13, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 26, 26, 26, 61, 61, 61, 61, 61, 61, 61, 61, 61, 9, 1, 1, 1, 1, 9, 9, 26, 61, 61, 61, 61, 61, 61, 61, 9, 9] 61
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 133
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040321 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(=NNC(=O)C2=CC3=CC=CC=C3C=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', 'Cl', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.am', '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.3', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 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
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 9, 9, 5, 9, 9, 9, 1, 1, 1, 1, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 9, 9, 8, 9, 1, 1, 6, 24, 24, 24, 24, 24, 24, 24, 1, 1] 61
rigid atoms, others: [32, 1, 3, 4, 33, 42, 11, 12, 13, 14, 43, 27] set([0, 2, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 65
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040321 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040321
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040321/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040321
Building REAL300000040322
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040322'
/scratch/stefan/7769621/working/building/REAL300000040322 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040322

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040322/0 /scratch/stefan/7769621/working/building/REAL300000040322 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 416)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/416
`/scratch/stefan/7769621/working/3D/416' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC(=O)C1=CC2=CC=CC=C2C=C1)

`REAL300000040322.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040322.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040322/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040322 none O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC(=O)C1=CC2=CC=CC=C2C=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', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1] 13
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 15, 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, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 23
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040322 none O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC(=O)C1=CC2=CC=CC=C2C=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', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 13, 13, 13, 13] 13
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35] set([36, 37, 38, 39, 40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 25
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040322 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040322
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040322/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040322
Building REAL300000040323
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040323'
/scratch/stefan/7769621/working/building/REAL300000040323 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040323

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040323/0 /scratch/stefan/7769621/working/building/REAL300000040323 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 417)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/417
`/scratch/stefan/7769621/working/3D/417' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=CN1)

`REAL300000040323.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040323.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040323/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040323 none O=C([O-])C1=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=CN1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', '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.2', 'N.pl3', '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, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [31, 31, 31, 31, 31, 21, 21, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 21, 6, 1, 1, 1, 1, 1, 1, 1, 31, 31] 31
rigid atoms, others: [32, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 34, 21, 22, 23, 24, 25, 33])
total number of confs: 50
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040323 none O=C([O-])C1=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=CN1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', '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.2', 'N.pl3', '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, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 7, 15, 31, 31, 31, 31, 31, 31, 31, 1, 1] 31
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 34, 21, 22, 23] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 63
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040323 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040323
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040323/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040323
Building REAL300000040324
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040324'
/scratch/stefan/7769621/working/building/REAL300000040324 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040324

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040324/0 /scratch/stefan/7769621/working/building/REAL300000040324 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 418)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/418
`/scratch/stefan/7769621/working/3D/418' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1(C(=O)[O-])CCC1)=NNC(=O)C1=CC2=CC=CC=C2C=C1)

`REAL300000040324.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040324.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040324/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040324 none CC(CC1(C(=O)[O-])CCC1)=NNC(=O)C1=CC2=CC=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', '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', 'H']
dock atom type numbers: [5, 1, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 11, 1, 1, 1, 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, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 23, 23, 63, 71, 71, 71, 71, 71, 71, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 63, 63, 71, 71, 71, 71, 71, 71, 7, 1, 1, 1, 1, 1, 1, 1] 71
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 223
number of broken/clashed sets: 48
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040324 none CC(CC1(C(=O)[O-])CCC1)=NNC(=O)C1=CC2=CC=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', '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', 'H']
dock atom type numbers: [5, 1, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 11, 1, 1, 1, 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, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 7, 1, 1, 1, 3, 3, 1, 1, 1, 13, 13, 29, 29, 29, 71, 71, 71, 71, 71, 71, 71, 71, 71, 13, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 29, 71, 71, 71, 71, 71, 71, 71] 71
rigid atoms, others: [32, 33, 2, 3, 4, 7, 8, 9, 34, 29, 30, 31] set([0, 1, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 166
number of broken/clashed sets: 48
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040324 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040324
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040324/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040324
Building REAL300000040325
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040325'
/scratch/stefan/7769621/working/building/REAL300000040325 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040325

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040325/0 /scratch/stefan/7769621/working/building/REAL300000040325 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 419)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/419
`/scratch/stefan/7769621/working/3D/419' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1)

`REAL300000040325.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040325.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040325/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040325 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 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, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 23, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48, 48, 48, 23, 7, 1, 1, 1, 1, 1, 1, 1] 48
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 14, 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, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 70
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040325 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 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, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 11, 11, 21, 21, 21, 48, 48, 48, 48, 48, 48, 48, 48, 48, 2, 2, 2, 1, 2, 2, 2, 1, 11, 21, 48, 48, 48, 48, 48, 48, 48] 48
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 9, 10, 11, 29] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 109
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040325 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040325
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040325/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040325
Building REAL300000040326
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040326'
/scratch/stefan/7769621/working/building/REAL300000040326 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040326

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040326/0 /scratch/stefan/7769621/working/building/REAL300000040326 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 420)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/420
`/scratch/stefan/7769621/working/3D/420' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Cl)C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=CC=C1)

`REAL300000040326.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040326.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040326/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040326 none O=C([O-])C1=C(Cl)C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [24, 24, 24, 24, 24, 24, 13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 13, 5, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24] 24
rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 34, 35, 22, 23, 24, 25, 26, 36])
total number of confs: 38
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040326 none O=C([O-])C1=C(Cl)C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 6, 10, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1] 24
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 22, 23, 24, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 56
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040326 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040326
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040326/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040326
Building REAL300000040327
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040327'
/scratch/stefan/7769621/working/building/REAL300000040327 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040327

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040327/0 /scratch/stefan/7769621/working/building/REAL300000040327 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 421)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/421
`/scratch/stefan/7769621/working/3D/421' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC(=O)C1=CC2=CC=CC=C2C=C1)

`REAL300000040327.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040327.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040327/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040327 none O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC(=O)C1=CC2=CC=CC=C2C=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', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1] 9
rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 16, 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, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 19
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040327 none O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC(=O)C1=CC2=CC=CC=C2C=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', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 9, 9, 9, 9, 9, 9, 9] 9
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([39, 40, 41, 42, 43, 44, 45, 46, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 16
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040327 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040327
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040327/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040327
Building REAL300000040328
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040328'
/scratch/stefan/7769621/working/building/REAL300000040328 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040328

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040328/0 /scratch/stefan/7769621/working/building/REAL300000040328 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 422)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/422
`/scratch/stefan/7769621/working/3D/422' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC(C(=O)[O-])=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1)

`REAL300000040328.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040328.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040328/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040328 none CN1N=CC(C(=O)[O-])=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 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, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 11, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 11, 5, 1, 1, 1, 1, 1, 1, 1] 19
rigid atoms, others: [32, 33, 34, 35, 36, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 24, 25, 26, 27, 28, 29])
total number of confs: 37
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040328 none CN1N=CC(C(=O)[O-])=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 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, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 6, 6, 8, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 6, 8, 19, 19, 19, 19, 19, 19, 19] 19
rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 27] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 49
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040328 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040328
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040328/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040328
Building REAL300000040329
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040329'
/scratch/stefan/7769621/working/building/REAL300000040329 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040329

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040329/0 /scratch/stefan/7769621/working/building/REAL300000040329 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 423)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/423
`/scratch/stefan/7769621/working/3D/423' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C=C1F)

`REAL300000040329.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040329.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040329/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040329 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C=C1F NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'F', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 27, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 27, 7, 1, 1, 1, 1, 1, 1, 1, 53] 53
rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28, 36])
total number of confs: 91
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040329 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C=C1F NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'F', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 7, 7, 13, 13, 13, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 7, 13, 53, 53, 53, 53, 53, 53, 53, 1] 53
rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 93
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040329 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040329
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040329/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040329
Building REAL300000040330
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040330'
/scratch/stefan/7769621/working/building/REAL300000040330 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040330

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040330/0 /scratch/stefan/7769621/working/building/REAL300000040330 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 424)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/424
`/scratch/stefan/7769621/working/3D/424' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C=CC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)O1)

`REAL300000040330.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040330.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040330/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040330 none O=C([O-])C=CC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [106, 106, 106, 106, 61, 61, 61, 61, 31, 31, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 61, 106, 106, 61, 61, 31, 7, 1, 1, 1, 1, 1, 1, 1] 106
rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 235
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040330 none O=C([O-])C=CC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [29, 12, 30, 12, 1, 1, 1, 1, 1, 1, 5, 5, 20, 20, 20, 61, 61, 61, 61, 61, 61, 61, 61, 61, 1, 12, 12, 1, 1, 5, 20, 61, 61, 61, 61, 61, 61, 61] 106
rigid atoms, others: [4, 5, 6, 7, 8, 9, 24, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 186
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040330 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040330
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040330/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040330
Building REAL300000040331
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040331'
/scratch/stefan/7769621/working/building/REAL300000040331 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040331

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040331/0 /scratch/stefan/7769621/working/building/REAL300000040331 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 425)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/425
`/scratch/stefan/7769621/working/3D/425' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC(C(=O)[O-])=CC=C1OC(C)C)

`REAL300000040331.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040331.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040331/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040331 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 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]
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: [9, 1, 9, 9, 31, 31, 31, 103, 103, 103, 103, 103, 103, 103, 103, 103, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 10, 21, 21, 10, 10, 10, 31, 103, 103, 103, 103, 103, 103, 103, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21] 159
rigid atoms, others: [1, 40, 41, 42, 16, 17, 18, 19, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 254
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040331 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 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]
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: [27, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 103, 103, 103, 103, 103, 103, 103, 103, 103, 153, 159, 159, 27, 27, 27, 7, 1, 1, 1, 1, 1, 1, 1, 103, 103, 103, 159, 159, 159, 159, 159, 159, 159] 159
rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 36, 38, 39] set([0, 1, 2, 3, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 259
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040331 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040331
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040331/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040331
Building REAL300000040332
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040332'
/scratch/stefan/7769621/working/building/REAL300000040332 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040332

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040332/0 /scratch/stefan/7769621/working/building/REAL300000040332 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 426)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/426
`/scratch/stefan/7769621/working/3D/426' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C2C(=CC=C1)CCC2=NNC(=O)C1=CC2=CC=CC=C2C=C1)

`REAL300000040332.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040332.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040332/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040332 none O=C([O-])C1=C2C(=CC=C1)CCC2=NNC(=O)C1=CC2=CC=CC=C2C=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', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1] 19
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 14, 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, 15, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 33
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040332 none O=C([O-])C1=C2C(=CC=C1)CCC2=NNC(=O)C1=CC2=CC=CC=C2C=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', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 1, 1, 3, 3, 3, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 3, 19, 19, 19, 19, 19, 19, 19] 19
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 2, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 30
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040332 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040332
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040332/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040332
Building REAL300000040333
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040333'
/scratch/stefan/7769621/working/building/REAL300000040333 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040333

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040333/0 /scratch/stefan/7769621/working/building/REAL300000040333 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 427)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/427
`/scratch/stefan/7769621/working/3D/427' -> `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=NNC(=O)C3=CC4=CC=CC=C4C=C3)C=C2)C=C1)

`REAL300000040333.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040333.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040333/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040333 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)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', 'N.am', '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', '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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 24, 28, 28, 23, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 23, 7, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28] 28
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 14, 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, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46])
total number of confs: 64
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: REAL300000040333 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)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', 'N.am', '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', '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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 11, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 3, 3, 3, 3, 1, 1, 5, 11, 28, 28, 28, 28, 28, 28, 28, 1, 1, 3, 3] 28
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 44, 43, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46])
total number of confs: 71
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040333 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)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', 'N.am', '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', '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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 9, 9, 15, 15, 15, 28, 28, 28, 28, 28, 28, 28, 28, 28, 3, 3, 1, 1, 1, 1, 3, 3, 9, 15, 28, 28, 28, 28, 28, 28, 28, 3, 3, 1, 1] 28
rigid atoms, others: [1, 3, 4, 5, 6, 7, 45, 46, 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])
total number of confs: 71
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040333 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040333
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040333/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040333
Building REAL300000040334
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040334'
/scratch/stefan/7769621/working/building/REAL300000040334 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040334

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040334/0 /scratch/stefan/7769621/working/building/REAL300000040334 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 428)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/428
`/scratch/stefan/7769621/working/3D/428' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CN=CC(C(=O)[O-])=C1)

`REAL300000040334.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040334.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040334/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040334 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [11, 1, 11, 11, 15, 15, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 11, 11, 15, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1] 33
rigid atoms, others: [1, 36, 37, 38, 16, 17, 18, 19, 20, 21, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 71
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040334 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 15, 7, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33] 33
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 36, 5, 38, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37])
total number of confs: 53
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040334 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040334
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040334/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040334
Building REAL300000040335
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040335'
/scratch/stefan/7769621/working/building/REAL300000040335 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040335

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040335/0 /scratch/stefan/7769621/working/building/REAL300000040335 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 429)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/429
`/scratch/stefan/7769621/working/3D/429' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2NC=C(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)C2=C1)

`REAL300000040335.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040335.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040335/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040335 none O=C([O-])C1=CC=C2NC=C(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', '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', 'C.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, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 17, 17, 17, 13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 13, 5, 1, 1, 1, 1, 1, 1, 1, 17] 17
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 25, 26, 27, 28, 29, 30, 31, 32, 40])
total number of confs: 31
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040335 none O=C([O-])C1=CC=C2NC=C(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', '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', 'C.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, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 6, 6, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 6, 8, 17, 17, 17, 17, 17, 17, 17, 1] 17
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 40, 25, 26, 27, 28, 29, 30] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 39
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040335 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040335
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040335/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040335
Building REAL300000040336
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040336'
/scratch/stefan/7769621/working/building/REAL300000040336 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040336

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040336/0 /scratch/stefan/7769621/working/building/REAL300000040336 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 430)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/430
`/scratch/stefan/7769621/working/3D/430' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C=N1)

`REAL300000040336.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040336.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040336/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040336 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', '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', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 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]
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, 14, 14, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 14, 7, 1, 1, 1, 1, 1, 1, 1, 29] 29
rigid atoms, others: [32, 33, 34, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 35, 22, 23, 24, 25, 26, 27])
total number of confs: 53
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040336 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', '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', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 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]
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, 7, 7, 11, 11, 11, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 7, 11, 29, 29, 29, 29, 29, 29, 29, 1] 29
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: 56
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040336 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040336
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040336/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040336
Building REAL300000040337
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040337'
/scratch/stefan/7769621/working/building/REAL300000040337 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040337

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040337/0 /scratch/stefan/7769621/working/building/REAL300000040337 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 431)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/431
`/scratch/stefan/7769621/working/3D/431' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C=C1O)

`REAL300000040337.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040337.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040337/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040337 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'O.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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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
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, 23, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 23, 7, 1, 1, 1, 1, 1, 1, 1, 43, 86] 86
rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28, 37, 36])
total number of confs: 161
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040337 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'O.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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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
86  conformations in input
total number of sets (complete confs): 86
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 6, 10, 43, 43, 43, 43, 43, 43, 43, 1, 2] 86
rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37])
total number of confs: 76
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040337 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040337
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040337/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040337
Building REAL300000040338
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040338'
/scratch/stefan/7769621/working/building/REAL300000040338 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040338

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040338/0 /scratch/stefan/7769621/working/building/REAL300000040338 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 432)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/432
`/scratch/stefan/7769621/working/3D/432' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C=C1C(=O)[O-])

`REAL300000040338.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040338.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040338/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040338 none CC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', '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', '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, 1, 1, 1, 1, 1, 8, 8, 1, 11, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [46, 46, 46, 46, 20, 20, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 20, 7, 1, 1, 1, 1, 1, 1, 1, 46] 46
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39])
total number of confs: 73
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040338 none CC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', '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', '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, 1, 1, 1, 1, 1, 8, 8, 1, 11, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 17, 17, 17, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 9, 17, 46, 46, 46, 46, 46, 46, 46, 1] 46
rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 20, 21, 22, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 98
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040338 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040338
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040338/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040338
Building REAL300000040339
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040339'
/scratch/stefan/7769621/working/building/REAL300000040339 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040339

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040339/0 /scratch/stefan/7769621/working/building/REAL300000040339 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 433)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/433
`/scratch/stefan/7769621/working/3D/433' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Cl)SC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=C1)

`REAL300000040339.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040339.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040339/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040339 none O=C([O-])C1=C(Cl)SC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 69, 30, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69, 30, 7, 1, 1, 1, 1, 1, 1, 1, 69] 69
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 23, 24, 25, 33])
total number of confs: 101
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040339 none O=C([O-])C1=C(Cl)SC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 13, 13, 30, 30, 30, 69, 69, 69, 69, 69, 69, 69, 69, 69, 1, 13, 30, 69, 69, 69, 69, 69, 69, 69, 1] 69
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 23, 33] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 140
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040339 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040339
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040339/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040339
Building REAL300000040340
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040340'
/scratch/stefan/7769621/working/building/REAL300000040340 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040340

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040340/0 /scratch/stefan/7769621/working/building/REAL300000040340 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 434)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/434
`/scratch/stefan/7769621/working/3D/434' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=C(C(=O)[O-])C=C1C)

`REAL300000040340.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040340.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040340/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040340 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [9, 1, 9, 9, 14, 14, 14, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 14, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 2, 2, 2] 33
rigid atoms, others: [1, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 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, 40, 41, 42])
total number of confs: 74
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040340 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [18, 18, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 33, 33, 18, 18, 33, 33, 33, 33, 33, 18, 18, 18, 7, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33] 33
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 36, 30, 31] set([0, 1, 2, 3, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42])
total number of confs: 125
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040340 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040340
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040340/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040340
Building REAL300000040341
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040341'
/scratch/stefan/7769621/working/building/REAL300000040341 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040341

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040341/0 /scratch/stefan/7769621/working/building/REAL300000040341 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 435)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/435
`/scratch/stefan/7769621/working/3D/435' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C(Cl)C=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1)

`REAL300000040341.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040341.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040341/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040341 none O=C([O-])C1=CN=C(Cl)C=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 16, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [23, 23, 23, 23, 23, 16, 23, 23, 23, 11, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 11, 7, 1, 1, 1, 1, 1, 1, 1] 23
rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 25, 26, 27, 28])
total number of confs: 58
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040341 none O=C([O-])C1=CN=C(Cl)C=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 16, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 6, 10, 23, 23, 23, 23, 23, 23, 23] 23
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 53
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040341 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040341
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040341/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040341
Building REAL300000040342
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040342'
/scratch/stefan/7769621/working/building/REAL300000040342 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040342

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040342/0 /scratch/stefan/7769621/working/building/REAL300000040342 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 436)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/436
`/scratch/stefan/7769621/working/3D/436' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1)

`REAL300000040342.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040342.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040342/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040342 none CN1N=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 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, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 29, 29, 19, 19, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 19, 5, 1, 1, 1, 1, 1, 1, 1] 29
rigid atoms, others: [32, 33, 34, 35, 36, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 24, 25, 26, 27, 28, 29])
total number of confs: 45
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040342 none CN1N=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 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, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 2, 2, 2, 1, 6, 12, 29, 29, 29, 29, 29, 29, 29] 29
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 27] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 66
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040342 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040342
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040342/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040342
Building REAL300000040343
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040343'
/scratch/stefan/7769621/working/building/REAL300000040343 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040343

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040343/0 /scratch/stefan/7769621/working/building/REAL300000040343 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 437)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/437
`/scratch/stefan/7769621/working/3D/437' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1)

`REAL300000040343.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040343.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040343/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040343 none CN1C=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 30, 30, 20, 20, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 20, 5, 1, 1, 1, 1, 1, 1, 1] 30
rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 46
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040343 none CN1C=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 7, 7, 14, 14, 13, 30, 30, 30, 30, 30, 30, 30, 30, 30, 2, 2, 2, 1, 1, 7, 14, 30, 30, 30, 30, 30, 30, 30] 30
rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 27, 28] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 75
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040343 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040343
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040343/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040343
Building REAL300000040344
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040344'
/scratch/stefan/7769621/working/building/REAL300000040344 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040344

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040344/0 /scratch/stefan/7769621/working/building/REAL300000040344 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 438)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/438
`/scratch/stefan/7769621/working/3D/438' -> `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=NNC(=O)C1=CC2=CC=CC=C2C=C1)

`REAL300000040344.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040344.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040344/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040344 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1 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.am', 'C.2', 'O.2', '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, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 19, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 19, 7, 1, 1, 1, 1, 1, 1, 1] 39
rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 15, 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, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 59
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040344 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1 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.am', 'C.2', 'O.2', '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, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 8, 8, 15, 15, 15, 39, 39, 39, 39, 39, 39, 39, 39, 39, 4, 4, 4, 4, 4, 4, 1, 1, 1, 8, 15, 39, 39, 39, 39, 39, 39, 39] 39
rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 10, 11, 12, 35, 7] set([0, 2, 8, 9, 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])
total number of confs: 92
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040344 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040344
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040344/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040344
Building REAL300000040345
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040345'
/scratch/stefan/7769621/working/building/REAL300000040345 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040345

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040345/0 /scratch/stefan/7769621/working/building/REAL300000040345 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 439)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/439
`/scratch/stefan/7769621/working/3D/439' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])C=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)O1)

`REAL300000040345.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040345.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040345/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040345 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.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']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 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
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [62, 62, 62, 62, 62, 62, 62, 32, 32, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 62, 32, 7, 1, 1, 1, 1, 1, 1, 1] 62
rigid atoms, others: [32, 33, 34, 35, 36, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 106
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040345 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.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']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 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
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 8, 8, 14, 14, 14, 62, 62, 62, 62, 62, 62, 62, 62, 62, 1, 2, 2, 2, 1, 8, 14, 62, 62, 62, 62, 62, 62, 62] 62
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 23, 27] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 109
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040345 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040345
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040345/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040345
Building REAL300000040346
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040346'
/scratch/stefan/7769621/working/building/REAL300000040346 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040346

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040346/0 /scratch/stefan/7769621/working/building/REAL300000040346 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 440)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/440
`/scratch/stefan/7769621/working/3D/440' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC(C(=O)[O-])=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)S1)

`REAL300000040346.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040346.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040346/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040346 none CCC1=CC(C(=O)[O-])=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 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, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 31, 31, 31, 31, 31, 32, 32, 15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 53, 53, 53, 53, 53, 31, 15, 7, 1, 1, 1, 1, 1, 1, 1] 53
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 186
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040346 none CCC1=CC(C(=O)[O-])=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 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, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 1, 1, 1, 1, 3, 3, 1, 1, 5, 5, 11, 11, 11, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 8, 8, 8, 7, 7, 1, 5, 11, 31, 31, 31, 31, 31, 31, 31] 53
rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 24, 30] set([0, 6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 93
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040346 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040346
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040346/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040346
Building REAL300000040347
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040347'
/scratch/stefan/7769621/working/building/REAL300000040347 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040347

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040347/0 /scratch/stefan/7769621/working/building/REAL300000040347 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 441)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/441
`/scratch/stefan/7769621/working/3D/441' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1)

`REAL300000040347.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040347.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040347/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040347 none COC1=CC=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 31, 31, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 107, 107, 31, 7, 1, 1, 1, 1, 1, 1, 1] 107
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 14, 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, 15, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 135
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040347 none COC1=CC=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 34, 34, 34, 107, 107, 107, 107, 107, 107, 107, 107, 107, 3, 3, 3, 1, 1, 1, 12, 34, 107, 107, 107, 107, 107, 107, 107] 107
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 195
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040347 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040347
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040347/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040347
Building REAL300000040348
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040348'
/scratch/stefan/7769621/working/building/REAL300000040348 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040348

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040348/0 /scratch/stefan/7769621/working/building/REAL300000040348 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 442)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/442
`/scratch/stefan/7769621/working/3D/442' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2SC=C(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)C2=C1)

`REAL300000040348.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040348.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040348/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040348 none O=C([O-])C1=CC=C2SC=C(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', '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', '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, 14, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 21, 21, 21, 21, 17, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 17, 5, 1, 1, 1, 1, 1, 1, 1, 21] 21
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 25, 26, 27, 28, 29, 30, 31, 39])
total number of confs: 35
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040348 none O=C([O-])C1=CC=C2SC=C(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', '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', '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, 14, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 6, 6, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 6, 10, 21, 21, 21, 21, 21, 21, 21, 1] 21
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 39, 25, 26, 27, 28, 29] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 51
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040348 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040348
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040348/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040348
Building REAL300000040349
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040349'
/scratch/stefan/7769621/working/building/REAL300000040349 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040349

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040349/0 /scratch/stefan/7769621/working/building/REAL300000040349 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 443)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/443
`/scratch/stefan/7769621/working/3D/443' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2CCCC(=NNC(=O)C3=CC4=CC=CC=C4C=C3)C2=C1)

`REAL300000040349.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040349.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040349/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040349 none O=C([O-])C1=CN=C2CCCC(=NNC(=O)C3=CC4=CC=CC=C4C=C3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', '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', '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, 8, 1, 5, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 1, 1, 1, 1, 1, 1, 1, 13] 13
rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42])
total number of confs: 25
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040349 none O=C([O-])C1=CN=C2CCCC(=NNC(=O)C3=CC4=CC=CC=C4C=C3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', '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', '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, 8, 1, 5, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 13, 13, 13, 13, 1] 13
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42] set([34, 35, 36, 37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24])
total number of confs: 23
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040349 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040349
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040349/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040349
Building REAL300000040350
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040350'
/scratch/stefan/7769621/working/building/REAL300000040350 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040350

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040350/0 /scratch/stefan/7769621/working/building/REAL300000040350 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 444)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/444
`/scratch/stefan/7769621/working/3D/444' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=COC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=C1)

`REAL300000040350.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040350.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040350/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040350 none O=C([O-])C1=COC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.am', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [37, 37, 37, 37, 37, 37, 18, 18, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 18, 7, 1, 1, 1, 1, 1, 1, 1, 37] 37
rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 33])
total number of confs: 65
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040350 none O=C([O-])C1=COC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.am', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 12, 12, 12, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 8, 12, 37, 37, 37, 37, 37, 37, 37, 1] 37
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 33] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 61
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040350 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040350
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040350/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040350
Building REAL300000040351
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040351'
/scratch/stefan/7769621/working/building/REAL300000040351 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040351

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040351/0 /scratch/stefan/7769621/working/building/REAL300000040351 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 445)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/445
`/scratch/stefan/7769621/working/3D/445' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(Br)C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=C1)

`REAL300000040351.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040351.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040351/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040351 none O=C([O-])C1=CC=C(Br)C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=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', 'N.am', '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', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 48, 26, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 26, 7, 1, 1, 1, 1, 1, 1, 1, 48] 48
rigid atoms, others: [32, 33, 34, 35, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 24, 25, 26, 27, 28, 36])
total number of confs: 74
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040351 none O=C([O-])C1=CC=C(Br)C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=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', 'N.am', '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', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 11, 11, 26, 26, 26, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 11, 26, 48, 48, 48, 48, 48, 48, 48, 1] 48
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 36] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 105
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040351 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040351
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040351/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040351
Building REAL300000040352
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040352'
/scratch/stefan/7769621/working/building/REAL300000040352 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040352

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040352/0 /scratch/stefan/7769621/working/building/REAL300000040352 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 446)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/446
`/scratch/stefan/7769621/working/3D/446' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C(C(=O)[O-])=C1)

`REAL300000040352.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040352.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040352/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040352 none CC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 6, 7, 7, 7, 7, 7, 7, 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
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, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 5, 1, 1, 1, 1, 1, 1, 1, 17] 17
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39])
total number of confs: 34
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040352 none CC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', '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', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 6, 7, 7, 7, 7, 7, 7, 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
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 3, 3, 1, 2, 2, 2, 1, 1, 6, 11, 17, 17, 17, 17, 17, 17, 17, 1] 17
rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 20, 21, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 53
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040352 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040352
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040352/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040352
Building REAL300000040353
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040353'
/scratch/stefan/7769621/working/building/REAL300000040353 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040353

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040353/0 /scratch/stefan/7769621/working/building/REAL300000040353 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 447)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/447
`/scratch/stefan/7769621/working/3D/447' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=CC=C1C(=O)[O-])

`REAL300000040353.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040353.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040353/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040353 none COC1=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', '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', '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, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 6, 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
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [110, 64, 64, 60, 33, 33, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 110, 110, 110, 110, 110, 64, 33, 7, 1, 1, 1, 1, 1, 1, 1, 64, 64] 110
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40])
total number of confs: 394
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040353 none COC1=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', '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', '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, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 6, 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
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 64, 64, 64, 64, 64, 64, 64, 64, 64, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 7, 21, 64, 64, 64, 64, 64, 64, 64, 1, 1] 110
rigid atoms, others: [1, 2, 3, 4, 5, 39, 40, 20, 21, 22, 23, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 123
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040353 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040353
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040353/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040353
Building REAL300000040354
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040354'
/scratch/stefan/7769621/working/building/REAL300000040354 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040354

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040354/0 /scratch/stefan/7769621/working/building/REAL300000040354 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 448)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/448
`/scratch/stefan/7769621/working/3D/448' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(F)=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C(F)=C1)

`REAL300000040354.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040354.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040354/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040354 none O=C([O-])C1=CC(F)=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.am', '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', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 15, 25, 16, 25, 25, 25, 15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 15, 7, 1, 1, 1, 1, 1, 1, 1, 25] 25
rigid atoms, others: [32, 33, 34, 35, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 23, 24, 25, 26, 27, 28, 36])
total number of confs: 110
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040354 none O=C([O-])C1=CC(F)=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.am', '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', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 7, 15, 25, 25, 25, 25, 25, 25, 25, 1] 25
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 36] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 63
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040354 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040354
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040354/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040354
Building REAL300000040355
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040355'
/scratch/stefan/7769621/working/building/REAL300000040355 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040355

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040355/0 /scratch/stefan/7769621/working/building/REAL300000040355 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 449)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/449
`/scratch/stefan/7769621/working/3D/449' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])NC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=C1)

`REAL300000040355.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040355.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040355/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040355 none CC1=C(C(=O)[O-])NC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 58, 32, 32, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 58, 32, 7, 1, 1, 1, 1, 1, 1, 1, 58] 58
rigid atoms, others: [32, 33, 34, 35, 36, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 23, 24, 25, 26, 27, 28, 29, 37])
total number of confs: 98
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040355 none CC1=C(C(=O)[O-])NC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 8, 8, 14, 14, 14, 58, 58, 58, 58, 58, 58, 58, 58, 58, 1, 2, 2, 2, 1, 8, 14, 58, 58, 58, 58, 58, 58, 58, 1] 58
rigid atoms, others: [0, 1, 2, 3, 37, 6, 7, 8, 23, 27] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 105
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040355 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040355
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040355/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040355
Building REAL300000040356
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040356'
/scratch/stefan/7769621/working/building/REAL300000040356 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040356

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040356/0 /scratch/stefan/7769621/working/building/REAL300000040356 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 450)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/450
`/scratch/stefan/7769621/working/3D/450' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC=CC=C2C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=C1O)

`REAL300000040356.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040356.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040356/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040356 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=C1O 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.ar', 'C.2', 'N.2', 'N.am', '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', 'O.3', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
1  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: [52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 23, 23, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 52, 52, 23, 5, 1, 1, 1, 1, 1, 1, 1, 104] 104
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 15, 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, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43])
total number of confs: 174
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040356 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=C1O 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.ar', 'C.2', 'N.2', 'N.am', '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', 'O.3', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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]
1  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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 22, 22, 22, 52, 52, 52, 52, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 1, 1, 10, 22, 52, 52, 52, 52, 52, 52, 52, 2] 104
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 33, 27, 28, 29, 30, 31] set([0, 2, 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: 115
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040356 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040356
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040356/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040356
Building REAL300000040357
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040357'
/scratch/stefan/7769621/working/building/REAL300000040357 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040357

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040357/0 /scratch/stefan/7769621/working/building/REAL300000040357 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 451)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/451
`/scratch/stefan/7769621/working/3D/451' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)SC(Cl)=C1)

`REAL300000040357.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040357.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040357/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040357 none O=C([O-])C1=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)SC(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 16, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 13, 5, 1, 1, 1, 1, 1, 1, 1, 21] 21
rigid atoms, others: [32, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 20, 21, 22, 23, 24, 25, 33])
total number of confs: 38
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040357 none O=C([O-])C1=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)SC(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 16, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 5, 5, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 5, 11, 21, 21, 21, 21, 21, 21, 21, 1] 21
rigid atoms, others: [1, 3, 4, 5, 33, 20, 21, 22, 23] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 52
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040357 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040357
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040357/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040357
Building REAL300000040358
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040358'
/scratch/stefan/7769621/working/building/REAL300000040358 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040358

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040358/0 /scratch/stefan/7769621/working/building/REAL300000040358 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 452)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/452
`/scratch/stefan/7769621/working/3D/452' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)SC=C1)

`REAL300000040358.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040358.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040358/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040358 none O=C([O-])C1=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)SC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 13, 5, 1, 1, 1, 1, 1, 1, 1, 21, 21] 21
rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 32, 20, 21, 22, 23, 24, 33])
total number of confs: 38
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040358 none O=C([O-])C1=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)SC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 5, 5, 11, 12, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 5, 11, 21, 21, 21, 21, 21, 21, 21, 1, 1] 21
rigid atoms, others: [32, 1, 3, 4, 5, 33, 20, 21, 22] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 54
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040358 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040358
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040358/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040358
Building REAL300000040359
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040359'
/scratch/stefan/7769621/working/building/REAL300000040359 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040359

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040359/0 /scratch/stefan/7769621/working/building/REAL300000040359 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 453)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/453
`/scratch/stefan/7769621/working/3D/453' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=CS1)

`REAL300000040359.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040359.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040359/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040359 none O=C([O-])C1=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=CS1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', '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.2', 'S.3', '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, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [31, 31, 31, 31, 31, 21, 21, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 21, 5, 1, 1, 1, 1, 1, 1, 1, 31] 31
rigid atoms, others: [32, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 21, 22, 23, 24, 25, 33])
total number of confs: 49
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040359 none O=C([O-])C1=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=CS1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', '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.2', 'S.3', '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, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 6, 6, 12, 12, 12, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 6, 12, 31, 31, 31, 31, 31, 31, 31, 1] 31
rigid atoms, others: [1, 3, 4, 5, 6, 33, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 66
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040359 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040359
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040359/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040359
Building REAL300000040360
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040360'
/scratch/stefan/7769621/working/building/REAL300000040360 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040360

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040360/0 /scratch/stefan/7769621/working/building/REAL300000040360 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 454)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/454
`/scratch/stefan/7769621/working/3D/454' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=CC=C1OCC(=O)[O-])

`REAL300000040360.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040360.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040360/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040360 none CCOC1=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=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.am', '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', '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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 63, 28, 28, 28, 8, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 100, 194, 200, 200, 86, 86, 86, 86, 86, 28, 8, 5, 1, 1, 1, 1, 1, 1, 1, 28, 28, 194, 194] 201
rigid atoms, others: [43, 37, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47])
total number of confs: 751
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040360 none CCOC1=CC(C=NNC(=O)C2=CC3=CC=CC=C3C=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.am', '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', '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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 1, 1, 1, 1, 1, 7, 7, 9, 9, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 9, 33, 46, 46, 15, 15, 15, 15, 15, 1, 7, 9, 28, 28, 28, 28, 28, 28, 28, 1, 1, 33, 33] 201
rigid atoms, others: [34, 3, 4, 5, 6, 44, 2, 45, 21, 22, 23, 24] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47])
total number of confs: 227
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040360 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040360
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040360/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040360
Building REAL300000040361
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040361'
/scratch/stefan/7769621/working/building/REAL300000040361 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040361

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040361/0 /scratch/stefan/7769621/working/building/REAL300000040361 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 455)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/455
`/scratch/stefan/7769621/working/3D/455' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1)

`REAL300000040361.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040361.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040361/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040361 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1 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', 'N.am', 'C.2', 'O.2', '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', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 26, 36, 26, 26, 26, 26, 67, 67, 67, 67, 67, 26, 17, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 67, 67, 67, 67, 26, 17, 7, 1, 1, 1, 1, 1, 1, 1] 67
rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 17, 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, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 203
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: REAL300000040361 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1 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', 'N.am', 'C.2', 'O.2', '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', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [19, 13, 19, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 24, 24, 36, 36, 36, 67, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 24, 36, 67, 67, 67, 67, 67, 67, 67] 67
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37, 29, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 167
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040361 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1 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', 'N.am', 'C.2', 'O.2', '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', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 1, 4, 4, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 4, 8, 26, 26, 26, 26, 26, 26, 26] 67
rigid atoms, others: [1, 3, 4, 5, 6, 12, 13, 14, 38] set([0, 2, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 77
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040361 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040361
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040361/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040361
Building REAL300000040362
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040362'
/scratch/stefan/7769621/working/building/REAL300000040362 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040362

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040362/0 /scratch/stefan/7769621/working/building/REAL300000040362 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 456)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/456
`/scratch/stefan/7769621/working/3D/456' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C)C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=C1C(=O)[O-])

`REAL300000040362.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040362.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040362/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040362 none COC1=CC=C(C)C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=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.am', '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', '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, 5, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 33, 33, 33, 33, 33, 33, 25, 25, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 57, 57, 57, 57, 57, 33, 33, 33, 33, 33, 25, 5, 1, 1, 1, 1, 1, 1, 1] 57
rigid atoms, others: [43, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 195
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040362 none COC1=CC=C(C)C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=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.am', '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', '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, 5, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 13, 13, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 3, 3, 3, 3, 3, 1, 1, 2, 2, 2, 3, 13, 33, 33, 33, 33, 33, 33, 33] 57
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 78
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040362 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040362
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040362/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040362
Building REAL300000040363
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040363'
/scratch/stefan/7769621/working/building/REAL300000040363 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040363

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040363/0 /scratch/stefan/7769621/working/building/REAL300000040363 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 457)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/457
`/scratch/stefan/7769621/working/3D/457' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C2=CC=C(F)C=C2C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=C1C(=O)[O-])

`REAL300000040363.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040363.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040363/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040363 none CN1C2=CC=C(F)C=C2C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=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.am', '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.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, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 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, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 5, 1, 1, 1, 1, 1, 1, 1] 19
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 37
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040363 none CN1C2=CC=C(F)C=C2C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=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.am', '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.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, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 3, 3, 2, 2, 2, 1, 1, 1, 6, 9, 19, 19, 19, 19, 19, 19, 19] 19
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 10, 7, 34, 25, 33, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 53
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040363 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040363
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040363/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040363
Building REAL300000040364
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040364'
/scratch/stefan/7769621/working/building/REAL300000040364 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040364

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040364/0 /scratch/stefan/7769621/working/building/REAL300000040364 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 458)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/458
`/scratch/stefan/7769621/working/3D/458' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=C(C(=O)[O-])C2=CC=CC=C2S1)

`REAL300000040364.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040364.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040364/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040364 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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.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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [6, 1, 6, 6, 15, 15, 15, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1] 36
rigid atoms, others: [1, 39, 40, 41, 42, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 75
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040364 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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.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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [23, 23, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 23, 23, 23, 6, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36] 36
rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 36, 38] set([0, 1, 2, 3, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42])
total number of confs: 55
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040364 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040364
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040364/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040364
Building REAL300000040365
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040365'
/scratch/stefan/7769621/working/building/REAL300000040365 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040365

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040365/0 /scratch/stefan/7769621/working/building/REAL300000040365 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 459)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/459
`/scratch/stefan/7769621/working/3D/459' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)O1)

`REAL300000040365.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040365.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040365/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040365 none O=C([O-])CCC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.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']
dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 193, 156, 66, 66, 66, 66, 33, 33, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 201, 201, 156, 156, 66, 66, 33, 7, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 737
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040365 none O=C([O-])CCC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.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']
dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 21, 23, 9, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 66, 66, 66, 66, 66, 66, 66, 66, 66, 1, 21, 21, 9, 9, 1, 1, 6, 22, 66, 66, 66, 66, 66, 66, 66] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 24, 29, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 231
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040365 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040365
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040365/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040365
Building REAL300000040366
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040366'
/scratch/stefan/7769621/working/building/REAL300000040366 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040366

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040366/0 /scratch/stefan/7769621/working/building/REAL300000040366 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 460)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/460
`/scratch/stefan/7769621/working/3D/460' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C2NC=C(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)C2=CC=C1)

`REAL300000040366.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040366.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040366/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040366 none O=C([O-])C1=C2NC=C(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 16, 16, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 16, 7, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32] 32
rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40])
total number of confs: 58
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040366 none O=C([O-])C1=C2NC=C(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 9, 10, 10, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 5, 9, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1] 32
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 38, 39, 40, 23, 24, 25, 26, 27, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 59
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040366 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040366
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040366/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040366
Building REAL300000040367
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040367'
/scratch/stefan/7769621/working/building/REAL300000040367 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040367

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040367/0 /scratch/stefan/7769621/working/building/REAL300000040367 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 461)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/461
`/scratch/stefan/7769621/working/3D/461' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1)

`REAL300000040367.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040367.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040367/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040367 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 3, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1] 13
rigid atoms, others: [1, 40, 41, 42, 43, 44, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 31
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040367 none CC(=NNC(=O)C1=CC2=CC=CC=C2C=C1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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]
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, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13] 13
rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 36, 38, 39] set([0, 1, 2, 3, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44])
total number of confs: 27
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040367 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040367
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040367/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040367
Building REAL300000040368
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040368'
/scratch/stefan/7769621/working/building/REAL300000040368 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040368

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040368/0 /scratch/stefan/7769621/working/building/REAL300000040368 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 462)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/462
`/scratch/stefan/7769621/working/3D/462' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)=CC=C2O1)

`REAL300000040368.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040368.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040368/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040368 none O=C([O-])C1=CC2=CC(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.ar', 'O.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, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 17, 17, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 17, 6, 1, 1, 1, 1, 1, 1, 1, 28, 28] 28
rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39])
total number of confs: 49
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040368 none O=C([O-])C1=CC2=CC(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.ar', 'O.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, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 14, 14, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 8, 14, 28, 28, 28, 28, 28, 28, 28, 1, 1] 28
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 38, 39, 23, 24, 25, 26, 27, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 63
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040368 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040368
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040368/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040368
Building REAL300000040369
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040369'
/scratch/stefan/7769621/working/building/REAL300000040369 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040369

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040369/0 /scratch/stefan/7769621/working/building/REAL300000040369 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 463)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/463
`/scratch/stefan/7769621/working/3D/463' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2C(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)=CC=CN12)

`REAL300000040369.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040369.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040369/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040369 none O=C([O-])C1=CN=C2C(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', '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.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 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]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 21, 21, 17, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 17, 5, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21] 21
rigid atoms, others: [32, 33, 34, 35, 36, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39])
total number of confs: 35
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040369 none O=C([O-])C1=CN=C2C(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', '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.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 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]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 6, 10, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1] 21
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 39, 23, 24, 25, 26, 27, 37] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 47
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040369 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040369
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040369/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040369
Building REAL300000040370
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040370'
/scratch/stefan/7769621/working/building/REAL300000040370 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040370

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040370/0 /scratch/stefan/7769621/working/building/REAL300000040370 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 464)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/464
`/scratch/stefan/7769621/working/3D/464' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(F)C=CC=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1)

`REAL300000040370.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040370.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040370/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040370 none O=C([O-])C1=C(F)C=CC=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 17, 17, 17, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 9, 5, 1, 1, 1, 1, 1, 1, 1] 17
rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 25, 26, 27, 28, 29])
total number of confs: 31
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040370 none O=C([O-])C1=C(F)C=CC=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 6, 8, 17, 17, 17, 17, 17, 17, 17] 17
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 41
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040370 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040370
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040370/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040370
Building REAL300000040371
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040371'
/scratch/stefan/7769621/working/building/REAL300000040371 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040371

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040371/0 /scratch/stefan/7769621/working/building/REAL300000040371 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 465)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/465
`/scratch/stefan/7769621/working/3D/465' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Br)C=CC=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1)

`REAL300000040371.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040371.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040371/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040371 none O=C([O-])C1=C(Br)C=CC=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1 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', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 11, 11, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 9, 5, 1, 1, 1, 1, 1, 1, 1] 11
rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 25, 26, 27, 28, 29])
total number of confs: 23
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040371 none O=C([O-])C1=C(Br)C=CC=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1 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', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 6, 6, 11, 11, 11, 11, 11, 11, 11] 11
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 25
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040371 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040371
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040371/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040371
Building REAL300000040372
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040372'
/scratch/stefan/7769621/working/building/REAL300000040372 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040372

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040372/0 /scratch/stefan/7769621/working/building/REAL300000040372 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 466)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/466
`/scratch/stefan/7769621/working/3D/466' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C2=C(C=C1)OCO2)

`REAL300000040372.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040372.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040372/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040372 none O=C([O-])C1=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C2=C(C=C1)OCO2 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 12, 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, 6, 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, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [27, 27, 27, 27, 11, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 11, 5, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 27
rigid atoms, others: [32, 33, 34, 35, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39])
total number of confs: 45
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040372 none O=C([O-])C1=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C2=C(C=C1)OCO2 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', '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', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 12, 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, 6, 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, 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: [3, 1, 3, 1, 1, 1, 6, 6, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 1, 6, 13, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1] 27
rigid atoms, others: [1, 3, 4, 5, 38, 39, 25, 20, 21, 22, 23, 24, 36, 26, 37] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 64
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040372 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040372
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040372/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040372
Building REAL300000040373
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040373'
/scratch/stefan/7769621/working/building/REAL300000040373 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040373

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040373/0 /scratch/stefan/7769621/working/building/REAL300000040373 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 467)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/467
`/scratch/stefan/7769621/working/3D/467' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=CC=C(C(=O)[O-])C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=C1)

`REAL300000040373.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040373.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040373/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040373 none N#CC1=CC=C(C(=O)[O-])C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 9, 5, 1, 1, 1, 1, 1, 1, 1, 19] 19
rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 25, 26, 27, 28, 29, 37])
total number of confs: 35
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040373 none N#CC1=CC=C(C(=O)[O-])C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 6, 6, 10, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 6, 10, 19, 19, 19, 19, 19, 19, 19, 1] 19
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 25, 26, 27, 37] set([7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 49
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040373 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040373
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040373/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040373
Building REAL300000040374
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040374'
/scratch/stefan/7769621/working/building/REAL300000040374 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040374

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040374/0 /scratch/stefan/7769621/working/building/REAL300000040374 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 468)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/468
`/scratch/stefan/7769621/working/3D/468' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C=C1Cl)

`REAL300000040374.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040374.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040374/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040374 none O=C([O-])COC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C=C1Cl 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.am', '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', 'C.ar', 'Cl', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 146, 59, 35, 59, 59, 19, 19, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 201, 201, 59, 59, 19, 5, 1, 1, 1, 1, 1, 1, 1, 59] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40])
total number of confs: 567
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040374 none O=C([O-])COC1=CC=C(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)C=C1Cl 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.am', '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', 'C.ar', 'Cl', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 35, 43, 9, 1, 1, 1, 1, 1, 1, 8, 8, 20, 20, 20, 59, 59, 59, 59, 59, 59, 59, 59, 59, 1, 1, 1, 35, 35, 1, 1, 8, 20, 59, 59, 59, 59, 59, 59, 59, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 40, 24, 25, 26, 29, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 247
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040374 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040374
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040374/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040374
Building REAL300000040375
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040375'
/scratch/stefan/7769621/working/building/REAL300000040375 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040375

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040375/0 /scratch/stefan/7769621/working/building/REAL300000040375 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 469)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/469
`/scratch/stefan/7769621/working/3D/469' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NSC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=C1C(=O)[O-])

`REAL300000040375.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040375.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040375/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040375 none CC1=NSC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', '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.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
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, 15, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 15, 5, 1, 1, 1, 1, 1, 1, 1] 21
rigid atoms, others: [32, 33, 34, 35, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 37
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040375 none CC1=NSC(C=NNC(=O)C2=CC3=CC=CC=C3C=C2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', '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.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 3, 3, 2, 2, 2, 6, 10, 21, 21, 21, 21, 21, 21, 21] 21
rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 57
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040375 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040375
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040375/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040375
Building REAL300000040376
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040376'
/scratch/stefan/7769621/working/building/REAL300000040376 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040376

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040376/0 /scratch/stefan/7769621/working/building/REAL300000040376 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 470)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/470
`/scratch/stefan/7769621/working/3D/470' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=C(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)C(F)=CC=C2S1)

`REAL300000040376.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040376.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040376/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040376 none O=C([O-])C1=CC2=C(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)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', 'N.am', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 21, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 21, 5, 1, 1, 1, 1, 1, 1, 1, 41, 41] 41
rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39])
total number of confs: 59
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040376 none O=C([O-])C1=CC2=C(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)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', 'N.am', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 9, 17, 17, 17, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 9, 17, 41, 41, 41, 41, 41, 41, 41, 1, 1] 41
rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 39, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 92
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040376 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040376
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040376/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040376
Building REAL300000040377
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040377'
/scratch/stefan/7769621/working/building/REAL300000040377 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040377

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040377/0 /scratch/stefan/7769621/working/building/REAL300000040377 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 471)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/471
`/scratch/stefan/7769621/working/3D/471' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1)

`REAL300000040377.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040377.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040377/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040377 none COC1=CC(C(=O)[O-])=CC=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 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, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [47, 47, 47, 43, 47, 47, 47, 47, 47, 47, 19, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 19, 7, 1, 1, 1, 1, 1, 1, 1] 47
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 14, 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, 15, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 91
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040377 none COC1=CC(C(=O)[O-])=CC=C1C=NNC(=O)C1=CC2=CC=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 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, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 16, 16, 16, 47, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4, 4, 1, 1, 1, 10, 16, 47, 47, 47, 47, 47, 47, 47] 47
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 94
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040377 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040377
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040377/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040377
Building REAL300000040378
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040378'
/scratch/stefan/7769621/working/building/REAL300000040378 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040378

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040378/0 /scratch/stefan/7769621/working/building/REAL300000040378 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 472)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/472
`/scratch/stefan/7769621/working/3D/472' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)=N2)C1)

`REAL300000040378.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040378.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040378/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040378 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 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
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, 168, 168, 168, 62, 168, 62, 62, 62, 35, 35, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 62, 168, 168, 168, 62, 62, 35, 7, 1, 1, 1, 1, 1, 1, 1, 168, 168] 168
rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 15, 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, 16, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43])
total number of confs: 373
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: REAL300000040378 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 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
168  conformations in input
total number of sets (complete confs): 168
using faster count positions algorithm for large data
unique positions, atoms: [22, 12, 22, 12, 12, 12, 1, 12, 1, 1, 1, 1, 1, 5, 5, 18, 18, 18, 62, 62, 62, 62, 62, 62, 62, 62, 62, 1, 12, 12, 12, 1, 1, 5, 18, 62, 62, 62, 62, 62, 62, 62, 12, 12] 168
rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 27, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 168
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040378 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC(=O)C3=CC4=CC=CC=C4C=C3)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 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
168  conformations in input
total number of sets (complete confs): 168
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 30, 30, 80, 80, 80, 168, 168, 168, 168, 168, 168, 168, 168, 168, 12, 1, 1, 1, 12, 12, 30, 80, 168, 168, 168, 168, 168, 168, 168, 1, 1] 168
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 42, 43, 28, 29, 30] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 346
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040378 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040378
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040378/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040378
Building REAL300000040379
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040379'
/scratch/stefan/7769621/working/building/REAL300000040379 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040379

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040379/0 /scratch/stefan/7769621/working/building/REAL300000040379 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 473)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/473
`/scratch/stefan/7769621/working/3D/473' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)C=C1)

`REAL300000040379.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040379.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040379/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040379 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 17, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 5, 1, 1, 1, 17, 17] 17
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 29, 30])
total number of confs: 27
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040379 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 17, 17, 16, 17, 17, 17, 17, 1, 1, 1, 1, 6, 10, 17, 17, 17, 1, 1] 17
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 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
/scratch/stefan/7769621/working/building/REAL300000040379 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040379
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040379/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040379
Building REAL300000040380
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040380'
/scratch/stefan/7769621/working/building/REAL300000040380 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040380

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040380/0 /scratch/stefan/7769621/working/building/REAL300000040380 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 474)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/474
`/scratch/stefan/7769621/working/3D/474' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=CC=C1C=NNC(=O)C1=CC=C(F)C=C1Br)

`REAL300000040380.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040380.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040380/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040380 none O=C([O-])COC1=CC=CC=C1C=NNC(=O)C1=CC=C(F)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.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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, 11, 1, 1, 1, 1, 15, 1, 1, 17, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
177  conformations in input
total number of sets (complete confs): 177
using faster count positions algorithm for large data
unique positions, atoms: [177, 177, 177, 132, 47, 47, 47, 25, 47, 47, 23, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 177, 177, 47, 47, 47, 47, 23, 7, 1, 1, 1] 177
rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 526
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040380 none O=C([O-])COC1=CC=CC=C1C=NNC(=O)C1=CC=C(F)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.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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, 11, 1, 1, 1, 1, 15, 1, 1, 17, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
177  conformations in input
total number of sets (complete confs): 177
using faster count positions algorithm for large data
unique positions, atoms: [75, 49, 75, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 16, 47, 47, 16, 32, 47, 47, 47, 49, 49, 1, 1, 1, 1, 6, 16, 47, 47, 47] 177
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28, 29] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34])
total number of confs: 404
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040380 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040380
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040380/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040380
Building REAL300000040381
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040381'
/scratch/stefan/7769621/working/building/REAL300000040381 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040381

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040381/0 /scratch/stefan/7769621/working/building/REAL300000040381 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 475)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/475
`/scratch/stefan/7769621/working/3D/475' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)C=C1)

`REAL300000040381.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040381.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040381/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040381 none O=C([O-])COC1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)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.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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, 11, 1, 1, 1, 1, 15, 1, 1, 17, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 128, 32, 32, 93, 93, 32, 32, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 93, 93, 201, 201, 93, 93, 32, 7, 1, 1, 1, 93, 93] 201
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 726
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040381 none O=C([O-])COC1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)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.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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, 11, 1, 1, 1, 1, 15, 1, 1, 17, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 14, 27, 3, 1, 1, 1, 1, 1, 1, 11, 11, 33, 33, 33, 93, 93, 54, 80, 93, 93, 93, 1, 1, 14, 14, 1, 1, 11, 33, 93, 93, 93, 1, 1] 201
rigid atoms, others: [33, 34, 4, 5, 6, 7, 8, 9, 22, 23, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32])
total number of confs: 386
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040381 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040381
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040381/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040381
Building REAL300000040382
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040382'
/scratch/stefan/7769621/working/building/REAL300000040382 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040382

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040382/0 /scratch/stefan/7769621/working/building/REAL300000040382 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 476)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/476
`/scratch/stefan/7769621/working/3D/476' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC=C1C=NNC(=O)C1=CC=C(F)C=C1Br)

`REAL300000040382.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040382.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040382/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040382 none O=C([O-])C1=CC=CC=C1C=NNC(=O)C1=CC=C(F)C=C1Br 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.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 21, 21, 21, 21, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 9, 5, 1, 1, 1] 21
rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27])
total number of confs: 35
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040382 none O=C([O-])C1=CC=CC=C1C=NNC(=O)C1=CC=C(F)C=C1Br 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.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 8, 21, 21, 12, 21, 21, 21, 21, 1, 1, 1, 1, 6, 8, 21, 21, 21] 21
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30])
total number of confs: 74
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040382 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040382
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040382/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040382
Building REAL300000040383
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040383'
/scratch/stefan/7769621/working/building/REAL300000040383 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040383

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040383/0 /scratch/stefan/7769621/working/building/REAL300000040383 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 477)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/477
`/scratch/stefan/7769621/working/3D/477' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC=C(C(=O)[O-])C=C1)

`REAL300000040383.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040383.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040383/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040383 none CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 4, 10, 10, 10, 19, 19, 15, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 19, 19, 19, 1, 1, 1, 1] 19
rigid atoms, others: [32, 1, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 59
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040383 none CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [7, 7, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 7, 19, 19, 19, 19, 19, 7, 7, 7, 5, 1, 1, 1, 19, 19, 19, 19] 19
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 75
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040383 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040383
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040383/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040383
Building REAL300000040384
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040384'
/scratch/stefan/7769621/working/building/REAL300000040384 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040384

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040384/0 /scratch/stefan/7769621/working/building/REAL300000040384 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 478)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/478
`/scratch/stefan/7769621/working/3D/478' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC=C(CC(=O)[O-])C=C1)

`REAL300000040384.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040384.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040384/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040384 none CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 6, 6, 13, 13, 13, 31, 31, 13, 31, 31, 31, 31, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 7, 7, 7, 13, 31, 31, 31, 1, 1, 2, 2, 1, 1] 47
rigid atoms, others: [32, 1, 35, 36, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34])
total number of confs: 147
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040384 none CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 14, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 14, 31, 31, 31, 31, 47, 47, 47, 31, 31, 14, 14, 14, 6, 1, 1, 1, 31, 31, 47, 47, 31, 31] 47
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36])
total number of confs: 147
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040384 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040384
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040384/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040384
Building REAL300000040385
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040385'
/scratch/stefan/7769621/working/building/REAL300000040385 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040385

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040385/0 /scratch/stefan/7769621/working/building/REAL300000040385 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 479)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/479
`/scratch/stefan/7769621/working/3D/479' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=CC(C=NNC(=O)C2=CC=C(F)C=C2Br)=C1)

`REAL300000040385.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040385.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040385/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040385 none O=C([O-])COC1=CC=CC(C=NNC(=O)C2=CC=C(F)C=C2Br)=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', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 123, 53, 53, 53, 53, 53, 27, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 53, 201, 201, 53, 53, 53, 27, 7, 1, 1, 1, 53] 201
rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 553
number of broken/clashed sets: 34
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040385 none O=C([O-])COC1=CC=CC(C=NNC(=O)C2=CC=C(F)C=C2Br)=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', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 42, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 16, 16, 16, 53, 53, 41, 42, 53, 53, 53, 1, 26, 26, 1, 1, 1, 8, 16, 53, 53, 53, 1] 201
rigid atoms, others: [34, 4, 5, 6, 7, 8, 9, 10, 23, 26, 27, 28] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 29, 30, 31, 32, 33])
total number of confs: 252
number of broken/clashed sets: 34
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040385 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040385
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040385/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040385
Building REAL300000040386
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040386'
/scratch/stefan/7769621/working/building/REAL300000040386 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040386

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040386/0 /scratch/stefan/7769621/working/building/REAL300000040386 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 480)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/480
`/scratch/stefan/7769621/working/3D/480' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)N1)

`REAL300000040386.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040386.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040386/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040386 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 8, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [35, 35, 35, 35, 35, 35, 23, 23, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 23, 5, 1, 1, 1, 35] 35
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 28])
total number of confs: 57
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040386 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 8, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 17, 17, 17, 35, 35, 24, 35, 35, 35, 35, 1, 1, 1, 9, 17, 35, 35, 35, 1] 35
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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/7769621/working/building/REAL300000040386 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040386
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040386/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040386
Building REAL300000040387
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040387'
/scratch/stefan/7769621/working/building/REAL300000040387 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040387

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040387/0 /scratch/stefan/7769621/working/building/REAL300000040387 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 481)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/481
`/scratch/stefan/7769621/working/3D/481' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC=C(C(=O)[O-])C=C1)

`REAL300000040387.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040387.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040387/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040387 none CCC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 1, 1, 11, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [15, 7, 1, 7, 7, 17, 17, 17, 32, 32, 17, 32, 32, 32, 32, 1, 1, 1, 1, 1, 2, 2, 1, 1, 15, 15, 15, 15, 15, 17, 32, 32, 32, 1, 1, 1, 1] 41
rigid atoms, others: [33, 2, 35, 36, 34, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 165
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040387 none CCC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 1, 1, 11, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [23, 16, 16, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 16, 32, 32, 16, 16, 32, 32, 32, 32, 23, 23, 23, 23, 23, 5, 1, 1, 1, 32, 32, 32, 32] 41
rigid atoms, others: [32, 5, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 182
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040387 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040387
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040387/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040387
Building REAL300000040388
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040388'
/scratch/stefan/7769621/working/building/REAL300000040388 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040388

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040388/0 /scratch/stefan/7769621/working/building/REAL300000040388 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 482)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/482
`/scratch/stefan/7769621/working/3D/482' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC=CC=C1C(=O)[O-])

`REAL300000040388.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040388.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040388/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040388 none CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 5, 13, 13, 13, 29, 29, 14, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 13, 29, 29, 29, 1, 1, 1, 1] 29
rigid atoms, others: [32, 1, 33, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 124
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040388 none CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [17, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 17, 29, 29, 29, 29, 29, 29, 29, 29, 17, 17, 17, 7, 1, 1, 1, 29, 29, 29, 29] 29
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 49
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040388 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040388
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040388/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040388
Building REAL300000040389
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040389'
/scratch/stefan/7769621/working/building/REAL300000040389 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040389

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040389/0 /scratch/stefan/7769621/working/building/REAL300000040389 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 483)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/483
`/scratch/stefan/7769621/working/3D/483' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC(C(=O)[O-])=CC=C1O)

`REAL300000040389.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040389.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040389/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040389 none CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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]
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: [9, 1, 9, 9, 19, 19, 19, 43, 43, 31, 43, 43, 43, 43, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 9, 9, 19, 43, 43, 43, 1, 1, 1, 2] 86
rigid atoms, others: [32, 1, 33, 14, 15, 16, 17, 20, 21, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 153
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040389 none CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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]
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: [23, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 23, 43, 43, 43, 43, 43, 43, 43, 43, 43, 23, 23, 23, 7, 1, 1, 1, 43, 43, 43, 86] 86
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 153
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040389 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040389
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040389/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040389
Building REAL300000040390
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040390'
/scratch/stefan/7769621/working/building/REAL300000040390 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040390

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040390/0 /scratch/stefan/7769621/working/building/REAL300000040390 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 484)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/484
`/scratch/stefan/7769621/working/3D/484' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC=CC(C(=O)[O-])=C1)

`REAL300000040390.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040390.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040390/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040390 none CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [9, 1, 9, 9, 11, 11, 11, 33, 33, 23, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 2, 2, 1, 9, 9, 9, 11, 33, 33, 33, 1, 1, 1, 1] 33
rigid atoms, others: [32, 1, 33, 14, 15, 16, 17, 18, 19, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 111
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040390 none CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [19, 19, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 33, 33, 33, 33, 33, 33, 33, 33, 19, 19, 19, 5, 1, 1, 1, 33, 33, 33, 33] 33
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 49
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040390 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040390
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040390/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040390
Building REAL300000040391
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040391'
/scratch/stefan/7769621/working/building/REAL300000040391 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040391

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040391/0 /scratch/stefan/7769621/working/building/REAL300000040391 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 485)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/485
`/scratch/stefan/7769621/working/3D/485' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CN1C=C(C=NNC(=O)C2=CC=C(F)C=C2Br)N=N1)

`REAL300000040391.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040391.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040391/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040391 none O=C([O-])CN1C=C(C=NNC(=O)C2=CC=C(F)C=C2Br)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 51, 51, 51, 29, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 89, 89, 51, 29, 7, 1, 1, 1] 89
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 273
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040391 none O=C([O-])CN1C=C(C=NNC(=O)C2=CC=C(F)C=C2Br)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [19, 8, 19, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 51, 51, 20, 32, 51, 51, 51, 1, 1, 8, 8, 1, 6, 20, 51, 51, 51] 89
rigid atoms, others: [3, 4, 5, 6, 7, 20, 21, 24] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 25, 26, 27, 28, 29])
total number of confs: 237
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040391 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040391
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040391/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040391
Building REAL300000040392
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040392'
/scratch/stefan/7769621/working/building/REAL300000040392 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040392

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040392/0 /scratch/stefan/7769621/working/building/REAL300000040392 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 486)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/486
`/scratch/stefan/7769621/working/3D/486' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC=C(C(=O)[O-])C(F)=C1)

`REAL300000040392.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040392.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040392/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040392 none CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 1, 11, 11, 33, 33, 33, 61, 61, 45, 61, 61, 61, 61, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 11, 11, 11, 33, 61, 61, 61, 1, 1, 1] 61
rigid atoms, others: [32, 1, 33, 14, 15, 16, 17, 18, 21, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 215
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040392 none CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 23, 61, 61, 61, 61, 61, 61, 61, 61, 61, 23, 23, 23, 7, 1, 1, 1, 61, 61, 61] 61
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33])
total number of confs: 89
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040392 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040392
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040392/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040392
Building REAL300000040393
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040393'
/scratch/stefan/7769621/working/building/REAL300000040393 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040393

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040393/0 /scratch/stefan/7769621/working/building/REAL300000040393 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 487)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/487
`/scratch/stefan/7769621/working/3D/487' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CSC(C=NNC(=O)C2=CC=C(F)C=C2Br)=C1)

`REAL300000040393.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040393.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040393/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040393 none O=C([O-])C1=CSC(C=NNC(=O)C2=CC=C(F)C=C2Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [37, 37, 37, 37, 37, 37, 25, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 25, 7, 1, 1, 1, 37] 37
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 27])
total number of confs: 61
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040393 none O=C([O-])C1=CSC(C=NNC(=O)C2=CC=C(F)C=C2Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 18, 19, 18, 37, 37, 18, 37, 37, 37, 37, 1, 1, 8, 18, 37, 37, 37, 1] 37
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26])
total number of confs: 140
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040393 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040393
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040393/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040393
Building REAL300000040394
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040394'
/scratch/stefan/7769621/working/building/REAL300000040394 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040394

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040394/0 /scratch/stefan/7769621/working/building/REAL300000040394 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 488)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/488
`/scratch/stefan/7769621/working/3D/488' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)C(Cl)=C1)

`REAL300000040394.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040394.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040394/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040394 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 23, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 23, 7, 1, 1, 1, 29] 29
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 45
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040394 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 14, 14, 14, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 8, 14, 29, 29, 29, 1] 29
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29])
total number of confs: 63
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040394 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040394
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040394/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040394
Building REAL300000040395
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040395'
/scratch/stefan/7769621/working/building/REAL300000040395 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040395

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040395/0 /scratch/stefan/7769621/working/building/REAL300000040395 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 489)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/489
`/scratch/stefan/7769621/working/3D/489' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C=NNC(=O)C2=CC=C(F)C=C2Br)=CC=C1O)

`REAL300000040395.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040395.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040395/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040395 none O=C([O-])C1=CC(C=NNC(=O)C2=CC=C(F)C=C2Br)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [32, 32, 32, 32, 32, 17, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 17, 7, 1, 1, 1, 32, 32, 64] 64
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31])
total number of confs: 117
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040395 none O=C([O-])C1=CC(C=NNC(=O)C2=CC=C(F)C=C2Br)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 8, 15, 15, 15, 32, 32, 26, 28, 32, 32, 32, 1, 1, 1, 1, 1, 8, 15, 32, 32, 32, 1, 1, 2] 64
rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 31])
total number of confs: 92
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040395 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040395
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040395/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040395
Building REAL300000040396
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040396'
/scratch/stefan/7769621/working/building/REAL300000040396 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040396

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040396/0 /scratch/stefan/7769621/working/building/REAL300000040396 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 490)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/490
`/scratch/stefan/7769621/working/3D/490' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC(C(=O)[O-])=CC=C1C)

`REAL300000040396.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040396.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040396/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040396 none CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [7, 1, 7, 7, 12, 12, 12, 27, 27, 19, 27, 27, 27, 27, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 7, 7, 12, 27, 27, 27, 1, 1, 1, 2, 2, 2] 27
rigid atoms, others: [32, 1, 33, 14, 15, 16, 17, 20, 21, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36])
total number of confs: 104
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040396 none CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [19, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 19, 27, 27, 27, 27, 27, 27, 27, 27, 27, 19, 19, 19, 7, 1, 1, 1, 27, 27, 27, 27, 27, 27] 27
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36])
total number of confs: 47
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040396 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040396
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040396/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040396
Building REAL300000040397
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040397'
/scratch/stefan/7769621/working/building/REAL300000040397 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040397

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040397/0 /scratch/stefan/7769621/working/building/REAL300000040397 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 491)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/491
`/scratch/stefan/7769621/working/3D/491' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC=C(C(=O)[O-])O1)

`REAL300000040397.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040397.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040397/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040397 none CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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: [4, 1, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 13, 13, 13, 1, 1] 13
rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 21
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040397 none CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 13, 13] 13
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30])
total number of confs: 23
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040397 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040397
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040397/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040397
Building REAL300000040398
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040398'
/scratch/stefan/7769621/working/building/REAL300000040398 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040398

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040398/0 /scratch/stefan/7769621/working/building/REAL300000040398 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 492)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/492
`/scratch/stefan/7769621/working/3D/492' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])C=C(C=NNC(=O)C2=CC=C(F)C=C2Br)N1)

`REAL300000040398.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040398.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040398/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040398 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)C2=CC=C(F)C=C2Br)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 19, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 19, 7, 1, 1, 1, 28] 28
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 46
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040398 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)C2=CC=C(F)C=C2Br)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 6, 6, 10, 11, 10, 28, 28, 18, 18, 28, 28, 28, 1, 2, 2, 2, 1, 6, 10, 28, 28, 28, 1] 28
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 21, 25, 31] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30])
total number of confs: 84
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040398 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040398
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040398/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040398
Building REAL300000040399
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040399'
/scratch/stefan/7769621/working/building/REAL300000040399 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040399

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040399/0 /scratch/stefan/7769621/working/building/REAL300000040399 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 493)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/493
`/scratch/stefan/7769621/working/3D/493' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1CC(=NNC(=O)C2=CC=C(F)C=C2Br)C1)

`REAL300000040399.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040399.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040399/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040399 none O=C([O-])C1CC(=NNC(=O)C2=CC=C(F)C=C2Br)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 21, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 7, 1, 1, 1, 21, 21] 21
rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 19, 20, 21, 22, 26, 27])
total number of confs: 34
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040399 none O=C([O-])C1CC(=NNC(=O)C2=CC=C(F)C=C2Br)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [3, 1, 3, 1, 1, 1, 1, 1, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 8, 21, 21, 21, 1, 1] 21
rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25])
total number of confs: 43
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040399 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040399
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040399/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040399
Building REAL300000040400
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040400'
/scratch/stefan/7769621/working/building/REAL300000040400 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040400

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040400/0 /scratch/stefan/7769621/working/building/REAL300000040400 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 494)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/494
`/scratch/stefan/7769621/working/3D/494' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(C=NNC(=O)C2=CC=C(F)C=C2Br)=C1)

`REAL300000040400.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040400.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040400/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040400 none O=C([O-])C1=CC=CC(C=NNC(=O)C2=CC=C(F)C=C2Br)=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', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 13, 13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 13, 7, 1, 1, 1, 23] 23
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 43
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040400 none O=C([O-])C1=CC=CC(C=NNC(=O)C2=CC=C(F)C=C2Br)=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', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 13, 13, 13, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 9, 13, 23, 23, 23, 1] 23
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 47
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040400 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040400
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040400/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040400
Building REAL300000040401
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040401'
/scratch/stefan/7769621/working/building/REAL300000040401 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040401

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040401/0 /scratch/stefan/7769621/working/building/REAL300000040401 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 495)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/495
`/scratch/stefan/7769621/working/3D/495' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CSC(C(=O)[O-])=C1)

`REAL300000040401.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040401.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040401/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040401 none CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 1, 7, 7, 9, 9, 9, 31, 31, 17, 31, 31, 31, 31, 1, 1, 1, 1, 1, 2, 2, 1, 7, 7, 7, 9, 31, 31, 31, 1, 1] 31
rigid atoms, others: [1, 14, 15, 16, 17, 18, 21, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 127
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040401 none CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 19, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 31, 31, 31, 31, 31, 31, 31, 19, 19, 19, 5, 1, 1, 1, 31, 31] 31
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30])
total number of confs: 45
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040401 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040401
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040401/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040401
Building REAL300000040402
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040402'
/scratch/stefan/7769621/working/building/REAL300000040402 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040402

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040402/0 /scratch/stefan/7769621/working/building/REAL300000040402 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 496)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/496
`/scratch/stefan/7769621/working/3D/496' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(F)C=C1Br)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C)

`REAL300000040402.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040402.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040402/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040402 none CC(=NNC(=O)C1=CC=C(F)C=C1Br)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [6, 1, 6, 6, 13, 13, 13, 32, 32, 13, 27, 32, 32, 32, 1, 1, 1, 1, 1, 1, 7, 10, 10, 1, 1, 1, 6, 6, 6, 13, 32, 32, 32, 1, 1, 7, 7, 2, 2, 2, 2, 2, 2] 42
rigid atoms, others: [1, 34, 33, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 162
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040402 none CC(=NNC(=O)C1=CC=C(F)C=C1Br)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [18, 18, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 18, 32, 32, 32, 32, 32, 42, 42, 42, 32, 32, 32, 18, 18, 18, 7, 1, 1, 1, 32, 32, 42, 42, 32, 32, 32, 32, 32, 32] 42
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 138
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040402 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040402
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040402/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040402
Building REAL300000040403
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040403'
/scratch/stefan/7769621/working/building/REAL300000040403 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040403

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040403/0 /scratch/stefan/7769621/working/building/REAL300000040403 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 497)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/497
`/scratch/stefan/7769621/working/3D/497' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCCCCCC(=O)[O-])=NNC(=O)C1=CC=C(F)C=C1Br)

`REAL300000040403.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040403.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040403/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040403 none CC(CCCCCCC(=O)[O-])=NNC(=O)C1=CC=C(F)C=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'H', '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, 5, 5, 5, 5, 1, 11, 11, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 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, 2, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 71, 80, 105, 129, 158, 201, 201, 201, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 71, 71, 91, 91, 102, 102, 144, 144, 161, 161, 198, 198, 7, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 1093
number of broken/clashed sets: 187
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040403 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040403
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040403/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040403
Building REAL300000040404
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040404'
/scratch/stefan/7769621/working/building/REAL300000040404 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040404

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040404/0 /scratch/stefan/7769621/working/building/REAL300000040404 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 498)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/498
`/scratch/stefan/7769621/working/3D/498' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(=NNC(=O)C2=CC=C(F)C=C2Br)CCC1CC(=O)[O-])

`REAL300000040404.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040404.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040404/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040404 none CC1C(=NNC(=O)C2=CC=C(F)C=C2Br)CCC1CC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 5, 5, 5, 5, 1, 11, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [17, 17, 17, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 21, 21, 21, 17, 17, 17, 17, 6, 1, 1, 1, 17, 17, 17, 17, 17, 21, 21] 21
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 52
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040404 none CC1C(=NNC(=O)C2=CC=C(F)C=C2Br)CCC1CC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 5, 5, 5, 5, 1, 11, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 5, 15, 17, 17, 17, 1, 1, 1, 1, 4, 5, 5, 2, 2, 2, 1, 5, 17, 17, 17, 1, 1, 1, 1, 1, 4, 4] 21
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 15, 16, 17, 18, 25, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 35, 36])
total number of confs: 83
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040404 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040404
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040404/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040404
Building REAL300000040405
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040405'
/scratch/stefan/7769621/working/building/REAL300000040405 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040405

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040405/0 /scratch/stefan/7769621/working/building/REAL300000040405 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 499)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/499
`/scratch/stefan/7769621/working/3D/499' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC(C(=O)[O-])=CS1)

`REAL300000040405.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040405.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040405/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040405 none CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 1, 11, 11, 20, 20, 19, 37, 37, 19, 34, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 19, 37, 37, 37, 1, 1] 37
rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 155
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040405 none CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 17, 37, 37, 37, 37, 37, 37, 37, 17, 17, 17, 7, 1, 1, 1, 37, 37] 37
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30])
total number of confs: 61
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040405 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040405
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040405/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040405
Building REAL300000040406
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040406'
/scratch/stefan/7769621/working/building/REAL300000040406 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040406

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040406/0 /scratch/stefan/7769621/working/building/REAL300000040406 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 500)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/500
`/scratch/stefan/7769621/working/3D/500' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(=NNC(=O)C2=CC=C(F)C=C2Br)CCC(C(=O)[O-])C1(C)C)

`REAL300000040406.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040406.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040406/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040406 none CC1C(=NNC(=O)C2=CC=C(F)C=C2Br)CCC(C(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.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, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 5, 5, 5, 1, 11, 11, 5, 5, 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, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
10  conformations in input
total number of sets (complete confs): 10
using default count positions algorithm for smaller data
unique positions, atoms: [10, 10, 10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 10
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 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])
total number of confs: 21
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040406 none CC1C(=NNC(=O)C2=CC=C(F)C=C2Br)CCC(C(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.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, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 5, 5, 5, 1, 11, 11, 5, 5, 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, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
10  conformations in input
total number of sets (complete confs): 10
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 5, 10, 10, 10, 10, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 2, 1, 5, 10, 10, 10, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 10
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 15, 16, 17, 18, 35, 21, 22, 23, 36, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 24, 25, 26, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42])
total number of confs: 60
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040406 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040406
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040406/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040406
Building REAL300000040407
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040407'
/scratch/stefan/7769621/working/building/REAL300000040407 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040407

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040407/0 /scratch/stefan/7769621/working/building/REAL300000040407 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 501)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/501
`/scratch/stefan/7769621/working/3D/501' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(C(=O)[O-])CCC1=NNC(=O)C1=CC=C(F)C=C1Br)

`REAL300000040407.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040407.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040407/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040407 none CC1CC(C(=O)[O-])CCC1=NNC(=O)C1=CC=C(F)C=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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, 11, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 1, 1, 1] 19
rigid atoms, others: [34, 35, 36, 12, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 32
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040407 none CC1CC(C(=O)[O-])CCC1=NNC(=O)C1=CC=C(F)C=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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, 11, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 8, 8, 8, 19, 19, 8, 13, 19, 19, 19, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 19, 19, 19] 19
rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 11, 32, 25, 26, 27, 28, 29, 30, 31] set([33, 34, 35, 36, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24])
total number of confs: 79
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040407 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040407
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040407/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040407
Building REAL300000040408
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040408'
/scratch/stefan/7769621/working/building/REAL300000040408 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040408

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040408/0 /scratch/stefan/7769621/working/building/REAL300000040408 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 502)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/502
`/scratch/stefan/7769621/working/3D/502' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(=NNC(=O)C2=CC=C(F)C=C2Br)CCC1C(=O)[O-])

`REAL300000040408.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040408.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040408/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040408 none CC1CC(=NNC(=O)C2=CC=C(F)C=C2Br)CCC1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 5, 5, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
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, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 1, 1, 1, 17, 17, 17, 17, 17] 17
rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36])
total number of confs: 30
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040408 none CC1CC(=NNC(=O)C2=CC=C(F)C=C2Br)CCC1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 5, 5, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 1, 8, 17, 17, 17, 1, 1, 1, 1, 1] 17
rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 32, 34, 16, 17, 18, 35, 33, 25, 26, 27, 36] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 28, 29, 30, 31])
total number of confs: 42
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040408 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040408
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040408/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040408
Building REAL300000040409
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040409'
/scratch/stefan/7769621/working/building/REAL300000040409 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040409

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040409/0 /scratch/stefan/7769621/working/building/REAL300000040409 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 503)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/503
`/scratch/stefan/7769621/working/3D/503' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C=NNC(=O)C2=CC=C(F)C=C2Br)=CN1)

`REAL300000040409.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040409.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040409/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040409 none O=C([O-])C1=CC(C=NNC(=O)C2=CC=C(F)C=C2Br)=CN1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 8, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [33, 33, 33, 33, 33, 23, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 23, 7, 1, 1, 1, 33, 33] 33
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 27, 28])
total number of confs: 53
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040409 none O=C([O-])C1=CC(C=NNC(=O)C2=CC=C(F)C=C2Br)=CN1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 8, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [2, 1, 2, 1, 1, 1, 1, 8, 8, 18, 18, 18, 33, 33, 23, 33, 33, 33, 33, 1, 1, 1, 8, 18, 33, 33, 33, 1, 1] 33
rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26])
total number of confs: 111
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040409 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040409
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040409/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040409
Building REAL300000040410
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040410'
/scratch/stefan/7769621/working/building/REAL300000040410 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040410

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040410/0 /scratch/stefan/7769621/working/building/REAL300000040410 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 504)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/504
`/scratch/stefan/7769621/working/3D/504' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1(C(=O)[O-])CCC1)=NNC(=O)C1=CC=C(F)C=C1Br)

`REAL300000040410.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040410.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040410/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040410 none CC(CC1(C(=O)[O-])CCC1)=NNC(=O)C1=CC=C(F)C=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 29, 29, 65, 67, 67, 67, 67, 67, 67, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 65, 65, 67, 67, 67, 67, 67, 67, 7, 1, 1, 1] 67
rigid atoms, others: [34, 35, 36, 12, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 204
number of broken/clashed sets: 47
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040410 none CC(CC1(C(=O)[O-])CCC1)=NNC(=O)C1=CC=C(F)C=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 7, 1, 1, 1, 3, 3, 1, 1, 1, 13, 13, 41, 41, 41, 67, 67, 41, 66, 67, 67, 67, 13, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 41, 67, 67, 67] 67
rigid atoms, others: [32, 2, 3, 4, 7, 8, 9, 27, 28, 29, 30, 31] set([0, 1, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 33, 34, 35, 36])
total number of confs: 271
number of broken/clashed sets: 47
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040410 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040410
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040410/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040410
Building REAL300000040411
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040411'
/scratch/stefan/7769621/working/building/REAL300000040411 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040411

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040411/0 /scratch/stefan/7769621/working/building/REAL300000040411 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 505)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/505
`/scratch/stefan/7769621/working/3D/505' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=C(F)C=C1Br)

`REAL300000040411.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040411.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040411/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040411 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=C(F)C=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 20, 20, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46, 46, 46, 20, 7, 1, 1, 1] 46
rigid atoms, others: [34, 35, 36, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 73
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040411 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=C(F)C=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 12, 12, 25, 25, 25, 46, 46, 41, 46, 46, 46, 46, 2, 2, 2, 1, 2, 2, 2, 1, 12, 25, 46, 46, 46] 46
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 27, 31] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36])
total number of confs: 143
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040411 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040411
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040411/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040411
Building REAL300000040412
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040412'
/scratch/stefan/7769621/working/building/REAL300000040412 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040412

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040412/0 /scratch/stefan/7769621/working/building/REAL300000040412 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 506)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/506
`/scratch/stefan/7769621/working/3D/506' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Cl)C(C=NNC(=O)C2=CC=C(F)C=C2Br)=CC=C1)

`REAL300000040412.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040412.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040412/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040412 none O=C([O-])C1=C(Cl)C(C=NNC(=O)C2=CC=C(F)C=C2Br)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [23, 23, 23, 23, 23, 23, 19, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 19, 7, 1, 1, 1, 23, 23, 23] 23
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 28, 29, 30])
total number of confs: 41
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040412 none O=C([O-])C1=C(Cl)C(C=NNC(=O)C2=CC=C(F)C=C2Br)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 23, 23, 12, 19, 23, 23, 23, 1, 1, 1, 6, 12, 23, 23, 23, 1, 1, 1] 23
rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 28, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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/7769621/working/building/REAL300000040412 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040412
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040412/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040412
Building REAL300000040413
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040413'
/scratch/stefan/7769621/working/building/REAL300000040413 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040413

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040413/0 /scratch/stefan/7769621/working/building/REAL300000040413 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 507)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/507
`/scratch/stefan/7769621/working/3D/507' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC(C(=O)[O-])=C1C=NNC(=O)C1=CC=C(F)C=C1Br)

`REAL300000040413.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040413.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040413/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040413 none CN1N=CC(C(=O)[O-])=C1C=NNC(=O)C1=CC=C(F)C=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 17, 17, 15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 15, 7, 1, 1, 1] 17
rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27])
total number of confs: 33
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040413 none CN1N=CC(C(=O)[O-])=C1C=NNC(=O)C1=CC=C(F)C=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 4, 4, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 4, 8, 17, 17, 17] 17
rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 25] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30])
total number of confs: 49
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040413 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040413
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040413/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040413
Building REAL300000040414
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040414'
/scratch/stefan/7769621/working/building/REAL300000040414 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040414

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040414/0 /scratch/stefan/7769621/working/building/REAL300000040414 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 508)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/508
`/scratch/stefan/7769621/working/3D/508' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)C=C1F)

`REAL300000040414.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040414.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040414/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040414 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)C=C1F NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 25, 25, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 25, 5, 1, 1, 1, 49] 49
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 83
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040414 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)C=C1F NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 49, 49, 15, 49, 49, 49, 49, 1, 1, 1, 1, 1, 6, 15, 49, 49, 49, 1] 49
rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29])
total number of confs: 207
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040414 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040414
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040414/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040414
Building REAL300000040415
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040415'
/scratch/stefan/7769621/working/building/REAL300000040415 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040415

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040415/0 /scratch/stefan/7769621/working/building/REAL300000040415 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 509)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/509
`/scratch/stefan/7769621/working/3D/509' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C=CC1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)O1)

`REAL300000040415.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040415.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040415/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040415 none O=C([O-])C=CC1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [101, 101, 101, 101, 61, 61, 61, 61, 37, 37, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 61, 101, 101, 61, 61, 37, 7, 1, 1, 1] 101
rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 237
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040415 none O=C([O-])C=CC1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [23, 9, 24, 9, 1, 1, 1, 1, 1, 1, 4, 4, 18, 18, 18, 61, 61, 18, 42, 61, 61, 61, 1, 10, 9, 1, 1, 4, 18, 61, 61, 61] 101
rigid atoms, others: [4, 5, 6, 7, 8, 9, 22, 25, 26] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 27, 28, 29, 30, 31])
total number of confs: 281
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040415 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040415
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040415/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040415
Building REAL300000040416
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040416'
/scratch/stefan/7769621/working/building/REAL300000040416 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040416

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040416/0 /scratch/stefan/7769621/working/building/REAL300000040416 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 510)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/510
`/scratch/stefan/7769621/working/3D/510' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C2C(=CC=C1)CCC2=NNC(=O)C1=CC=C(F)C=C1Br)

`REAL300000040416.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040416.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040416/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040416 none O=C([O-])C1=C2C(=CC=C1)CCC2=NNC(=O)C1=CC=C(F)C=C1Br 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', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1] 13
rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 23
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040416 none O=C([O-])C1=C2C(=CC=C1)CCC2=NNC(=O)C1=CC=C(F)C=C1Br 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', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 5, 12, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13] 13
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30] set([0, 32, 2, 33, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31])
total number of confs: 50
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040416 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040416
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040416/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040416
Building REAL300000040417
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040417'
/scratch/stefan/7769621/working/building/REAL300000040417 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040417

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040417/0 /scratch/stefan/7769621/working/building/REAL300000040417 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 511)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/511
`/scratch/stefan/7769621/working/3D/511' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CN=CC(C(=O)[O-])=C1)

`REAL300000040417.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040417.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040417/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040417 none CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 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: [9, 1, 9, 9, 11, 11, 11, 33, 33, 18, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 2, 2, 1, 9, 9, 9, 11, 33, 33, 33, 1, 1, 1] 33
rigid atoms, others: [32, 1, 14, 15, 16, 17, 18, 19, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 130
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040417 none CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 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: [19, 19, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 33, 33, 33, 33, 33, 33, 33, 33, 19, 19, 19, 5, 1, 1, 1, 33, 33, 33] 33
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29] set([0, 1, 2, 3, 5, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 49
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040417 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040417
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040417/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040417
Building REAL300000040418
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040418'
/scratch/stefan/7769621/working/building/REAL300000040418 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040418

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040418/0 /scratch/stefan/7769621/working/building/REAL300000040418 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 512)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/512
`/scratch/stefan/7769621/working/3D/512' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)C=N1)

`REAL300000040418.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040418.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040418/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040418 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)C=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [37, 37, 37, 37, 37, 37, 19, 19, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 19, 5, 1, 1, 1, 37] 37
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 29])
total number of confs: 65
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040418 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)C=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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]
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: [2, 1, 2, 1, 1, 1, 1, 1, 10, 10, 22, 22, 22, 37, 37, 25, 37, 37, 37, 37, 1, 1, 1, 1, 10, 22, 37, 37, 37, 1] 37
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: 124
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040418 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040418
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040418/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040418
Building REAL300000040419
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040419'
/scratch/stefan/7769621/working/building/REAL300000040419 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040419

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040419/0 /scratch/stefan/7769621/working/building/REAL300000040419 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 513)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/513
`/scratch/stefan/7769621/working/3D/513' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)C=C1O)

`REAL300000040419.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040419.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040419/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040419 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)C=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
84  conformations in input
total number of sets (complete confs): 84
using faster count positions algorithm for large data
unique positions, atoms: [42, 42, 42, 42, 42, 42, 24, 24, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 24, 6, 1, 1, 1, 42, 84] 84
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 151
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040419 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)C=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
84  conformations in input
total number of sets (complete confs): 84
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 8, 8, 17, 17, 17, 42, 42, 34, 42, 42, 42, 42, 1, 1, 1, 1, 1, 8, 17, 42, 42, 42, 1, 2] 84
rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 31])
total number of confs: 131
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040419 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040419
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040419/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040419
Building REAL300000040420
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040420'
/scratch/stefan/7769621/working/building/REAL300000040420 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040420

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040420/0 /scratch/stefan/7769621/working/building/REAL300000040420 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 514)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/514
`/scratch/stefan/7769621/working/3D/514' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)C=C1C(=O)[O-])

`REAL300000040420.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040420.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040420/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040420 none CC1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)C=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 45, 45, 44, 23, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 23, 7, 1, 1, 1, 45] 45
rigid atoms, others: [32, 8, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 72
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040420 none CC1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)C=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 8, 8, 23, 23, 23, 45, 45, 35, 35, 45, 45, 45, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 8, 23, 45, 45, 45, 1] 45
rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 18, 19, 20, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32])
total number of confs: 125
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040420 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040420
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040420/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040420
Building REAL300000040421
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040421'
/scratch/stefan/7769621/working/building/REAL300000040421 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040421

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040421/0 /scratch/stefan/7769621/working/building/REAL300000040421 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 515)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/515
`/scratch/stefan/7769621/working/3D/515' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC=C(C(=O)[O-])C=C1C)

`REAL300000040421.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040421.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040421/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040421 none CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 9, 9, 19, 19, 19, 27, 27, 19, 27, 27, 27, 27, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 9, 19, 27, 27, 27, 1, 1, 1, 2, 2, 2] 27
rigid atoms, others: [32, 1, 33, 14, 15, 16, 17, 18, 21, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36])
total number of confs: 101
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040421 none CC(=NNC(=O)C1=CC=C(F)C=C1Br)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 13, 27, 27, 13, 13, 27, 27, 27, 27, 27, 13, 13, 13, 7, 1, 1, 1, 27, 27, 27, 27, 27, 27] 27
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36])
total number of confs: 121
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040421 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040421
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040421/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040421
Building REAL300000040422
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040422'
/scratch/stefan/7769621/working/building/REAL300000040422 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040422

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040422/0 /scratch/stefan/7769621/working/building/REAL300000040422 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 516)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/516
`/scratch/stefan/7769621/working/3D/516' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=C(F)C=C1Br)

`REAL300000040422.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040422.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040422/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040422 none CN1N=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=C(F)C=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 23, 23, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 23, 5, 1, 1, 1] 31
rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27])
total number of confs: 47
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040422 none CN1N=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=C(F)C=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 16, 31, 31, 31, 31, 31, 30, 31, 2, 2, 2, 1, 6, 16, 31, 31, 31] 31
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30])
total number of confs: 75
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040422 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040422
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040422/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040422
Building REAL300000040423
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040423'
/scratch/stefan/7769621/working/building/REAL300000040423 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040423

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040423/0 /scratch/stefan/7769621/working/building/REAL300000040423 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 517)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/517
`/scratch/stefan/7769621/working/3D/517' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=C(F)C=C1Br)

`REAL300000040423.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040423.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040423/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040423 none CN1C=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=C(F)C=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 19, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 19, 7, 1, 1, 1] 27
rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 47
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040423 none CN1C=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=C(F)C=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 6, 6, 14, 14, 14, 27, 27, 19, 26, 27, 27, 27, 2, 2, 2, 1, 1, 6, 14, 27, 27, 27] 27
rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 25, 26] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31])
total number of confs: 98
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040423 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040423
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040423/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040423
Building REAL300000040424
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040424'
/scratch/stefan/7769621/working/building/REAL300000040424 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040424

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040424/0 /scratch/stefan/7769621/working/building/REAL300000040424 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 518)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/518
`/scratch/stefan/7769621/working/3D/518' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])C=C(C=NNC(=O)C2=CC=C(F)C=C2Br)O1)

`REAL300000040424.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040424.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040424/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040424 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)C2=CC=C(F)C=C2Br)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [56, 56, 56, 56, 56, 56, 56, 33, 33, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 56, 33, 7, 1, 1, 1] 56
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 91
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040424 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)C2=CC=C(F)C=C2Br)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 10, 10, 22, 22, 22, 56, 56, 56, 56, 56, 56, 56, 1, 2, 2, 2, 1, 10, 22, 56, 56, 56] 56
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 21, 25] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30])
total number of confs: 111
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040424 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040424
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040424/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040424
Building REAL300000040425
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040425'
/scratch/stefan/7769621/working/building/REAL300000040425 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040425

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040425/0 /scratch/stefan/7769621/working/building/REAL300000040425 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 519)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/519
`/scratch/stefan/7769621/working/3D/519' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC(C(=O)[O-])=C(C=NNC(=O)C2=CC=C(F)C=C2Br)S1)

`REAL300000040425.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040425.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040425/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040425 none CCC1=CC(C(=O)[O-])=C(C=NNC(=O)C2=CC=C(F)C=C2Br)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [59, 27, 27, 27, 27, 27, 35, 35, 17, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 27, 59, 59, 59, 59, 59, 27, 17, 7, 1, 1, 1] 59
rigid atoms, others: [32, 33, 12, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 245
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040425 none CCC1=CC(C(=O)[O-])=C(C=NNC(=O)C2=CC=C(F)C=C2Br)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 1, 1, 1, 1, 3, 3, 1, 1, 5, 5, 11, 11, 11, 27, 27, 19, 23, 27, 27, 27, 1, 8, 8, 8, 7, 7, 1, 5, 11, 27, 27, 27] 59
rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 22, 28] set([0, 6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33])
total number of confs: 108
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040425 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040425
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040425/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040425
Building REAL300000040426
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040426'
/scratch/stefan/7769621/working/building/REAL300000040426 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040426

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040426/0 /scratch/stefan/7769621/working/building/REAL300000040426 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 520)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/520
`/scratch/stefan/7769621/working/3D/520' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=C(F)C=C1Br)

`REAL300000040426.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040426.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040426/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040426 none COC1=CC=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=C(F)C=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 95, 95, 95, 95, 95, 95, 95, 25, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 95, 95, 95, 25, 7, 1, 1, 1] 95
rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 125
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040426 none COC1=CC=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=C(F)C=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 12, 12, 38, 38, 38, 95, 95, 61, 79, 95, 95, 95, 4, 4, 4, 1, 1, 1, 12, 38, 95, 95, 95] 95
rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 27, 28, 29] set([0, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34])
total number of confs: 320
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040426 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040426
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040426/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040426
Building REAL300000040427
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040427'
/scratch/stefan/7769621/working/building/REAL300000040427 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040427

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040427/0 /scratch/stefan/7769621/working/building/REAL300000040427 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 521)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/521
`/scratch/stefan/7769621/working/3D/521' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=COC(C=NNC(=O)C2=CC=C(F)C=C2Br)=C1)

`REAL300000040427.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040427.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040427/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040427 none O=C([O-])C1=COC(C=NNC(=O)C2=CC=C(F)C=C2Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [35, 35, 35, 35, 35, 35, 23, 23, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 23, 5, 1, 1, 1, 35] 35
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 27])
total number of confs: 57
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040427 none O=C([O-])C1=COC(C=NNC(=O)C2=CC=C(F)C=C2Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 16, 17, 16, 35, 35, 17, 35, 35, 35, 35, 1, 1, 8, 16, 35, 35, 35, 1] 35
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26])
total number of confs: 130
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040427 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040427
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040427/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040427
Building REAL300000040428
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040428'
/scratch/stefan/7769621/working/building/REAL300000040428 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040428

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040428/0 /scratch/stefan/7769621/working/building/REAL300000040428 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 522)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/522
`/scratch/stefan/7769621/working/3D/522' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)C(C(=O)[O-])=C1)

`REAL300000040428.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040428.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040428/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040428 none CC1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 5, 1, 1, 1, 21] 21
rigid atoms, others: [32, 8, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 35
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040428 none CC1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 8, 21, 21, 8, 21, 21, 21, 21, 1, 1, 3, 3, 1, 2, 2, 2, 1, 1, 6, 8, 21, 21, 21, 1] 21
rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 18, 19, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32])
total number of confs: 100
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040428 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040428
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040428/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040428
Building REAL300000040429
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040429'
/scratch/stefan/7769621/working/building/REAL300000040429 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040429

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040429/0 /scratch/stefan/7769621/working/building/REAL300000040429 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 523)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/523
`/scratch/stefan/7769621/working/3D/523' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)C2=CC=C(F)C=C2Br)=CC=C1C(=O)[O-])

`REAL300000040429.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040429.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040429/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040429 none COC1=CC(C=NNC(=O)C2=CC=C(F)C=C2Br)=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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
109  conformations in input
total number of sets (complete confs): 109
using faster count positions algorithm for large data
unique positions, atoms: [109, 92, 92, 87, 36, 36, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 92, 92, 92, 92, 109, 109, 109, 109, 109, 92, 36, 7, 1, 1, 1, 92, 92] 109
rigid atoms, others: [32, 8, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 250
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040429 none COC1=CC(C=NNC(=O)C2=CC=C(F)C=C2Br)=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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
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, 11, 11, 39, 39, 39, 92, 92, 44, 79, 92, 90, 92, 1, 1, 1, 1, 3, 3, 4, 4, 4, 1, 11, 39, 92, 92, 92, 1, 1] 109
rigid atoms, others: [1, 2, 3, 4, 5, 33, 34, 18, 19, 20, 21, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32])
total number of confs: 337
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040429 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040429
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040429/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040429
Building REAL300000040430
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040430'
/scratch/stefan/7769621/working/building/REAL300000040430 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040430

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040430/0 /scratch/stefan/7769621/working/building/REAL300000040430 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 524)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/524
`/scratch/stefan/7769621/working/3D/524' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])NC(C=NNC(=O)C2=CC=C(F)C=C2Br)=C1)

`REAL300000040430.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040430.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040430/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040430 none CC1=C(C(=O)[O-])NC(C=NNC(=O)C2=CC=C(F)C=C2Br)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [56, 56, 56, 56, 56, 56, 56, 31, 31, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 56, 31, 7, 1, 1, 1, 56] 56
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 90
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040430 none CC1=C(C(=O)[O-])NC(C=NNC(=O)C2=CC=C(F)C=C2Br)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 11, 11, 26, 26, 26, 56, 56, 56, 56, 56, 56, 56, 1, 2, 2, 2, 1, 11, 26, 56, 56, 56, 1] 56
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 21, 25, 31] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30])
total number of confs: 113
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040430 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040430
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040430/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040430
Building REAL300000040431
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040431'
/scratch/stefan/7769621/working/building/REAL300000040431 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040431

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040431/0 /scratch/stefan/7769621/working/building/REAL300000040431 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 525)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/525
`/scratch/stefan/7769621/working/3D/525' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NNC(=O)C2=CC=C(F)C=C2Br)SC=C1)

`REAL300000040431.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040431.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040431/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040431 none O=C([O-])C1=C(C=NNC(=O)C2=CC=C(F)C=C2Br)SC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 14, 1, 1, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [25, 25, 25, 25, 17, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 17, 7, 1, 1, 1, 25, 25] 25
rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 19, 20, 21, 22, 26, 27])
total number of confs: 43
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040431 none O=C([O-])C1=C(C=NNC(=O)C2=CC=C(F)C=C2Br)SC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 14, 1, 1, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [3, 1, 3, 1, 1, 1, 5, 5, 11, 11, 11, 25, 25, 11, 20, 25, 25, 25, 1, 1, 1, 5, 11, 25, 25, 25, 1, 1] 25
rigid atoms, others: [1, 3, 4, 5, 18, 19, 20, 26, 27] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25])
total number of confs: 100
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040431 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040431
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040431/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040431
Building REAL300000040432
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040432'
/scratch/stefan/7769621/working/building/REAL300000040432 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040432

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040432/0 /scratch/stefan/7769621/working/building/REAL300000040432 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 526)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/526
`/scratch/stefan/7769621/working/3D/526' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C=NNC(=O)C2=CC=C(F)C=C2Br)=CS1)

`REAL300000040432.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040432.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040432/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040432 none O=C([O-])C1=CC(C=NNC(=O)C2=CC=C(F)C=C2Br)=CS1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 14, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [35, 35, 35, 35, 35, 21, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 21, 7, 1, 1, 1, 35] 35
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 27])
total number of confs: 57
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040432 none O=C([O-])C1=CC(C=NNC(=O)C2=CC=C(F)C=C2Br)=CS1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 14, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [2, 1, 2, 1, 1, 1, 1, 8, 8, 20, 20, 20, 35, 35, 34, 35, 35, 35, 35, 1, 1, 1, 8, 20, 35, 35, 35, 1] 35
rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26])
total number of confs: 85
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040432 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040432
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040432/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040432
Building REAL300000040433
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040433'
/scratch/stefan/7769621/working/building/REAL300000040433 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040433

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040433/0 /scratch/stefan/7769621/working/building/REAL300000040433 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 527)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/527
`/scratch/stefan/7769621/working/3D/527' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCC1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)O1)

`REAL300000040433.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040433.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040433/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040433 none O=C([O-])CCC1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 193, 163, 80, 80, 80, 80, 36, 36, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 80, 201, 201, 163, 163, 80, 80, 36, 7, 1, 1, 1] 201
rigid atoms, others: [32, 33, 12, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 705
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040433 none O=C([O-])CCC1=CC=C(C=NNC(=O)C2=CC=C(F)C=C2Br)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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: [29, 21, 21, 9, 1, 1, 1, 1, 1, 1, 8, 8, 27, 27, 27, 80, 80, 80, 80, 80, 80, 80, 1, 21, 21, 9, 9, 1, 1, 8, 27, 80, 80, 80] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 22, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33])
total number of confs: 246
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040433 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040433
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040433/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040433
Building REAL300000040434
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040434'
/scratch/stefan/7769621/working/building/REAL300000040434 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040434

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040434/0 /scratch/stefan/7769621/working/building/REAL300000040434 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 528)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/528
`/scratch/stefan/7769621/working/3D/528' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(F)C=CC=C1C=NNC(=O)C1=CC=C(F)C=C1Br)

`REAL300000040434.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040434.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040434/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040434 none O=C([O-])C1=C(F)C=CC=C1C=NNC(=O)C1=CC=C(F)C=C1Br NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 21, 21, 21, 21, 21, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 9, 5, 1, 1, 1] 21
rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27])
total number of confs: 35
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040434 none O=C([O-])C1=C(F)C=CC=C1C=NNC(=O)C1=CC=C(F)C=C1Br NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 8, 21, 21, 13, 21, 21, 21, 21, 1, 1, 1, 6, 8, 21, 21, 21] 21
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30])
total number of confs: 75
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040434 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040434
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040434/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040434
Building REAL300000040435
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040435'
/scratch/stefan/7769621/working/building/REAL300000040435 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040435

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040435/0 /scratch/stefan/7769621/working/building/REAL300000040435 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 529)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/529
`/scratch/stefan/7769621/working/3D/529' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=CC=C(C(=O)[O-])C(C=NNC(=O)C2=CC=C(F)C=C2Br)=C1)

`REAL300000040435.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040435.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040435/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040435 none N#CC1=CC=C(C(=O)[O-])C(C=NNC(=O)C2=CC=C(F)C=C2Br)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 21, 21, 21, 21, 21, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 9, 5, 1, 1, 1, 21] 21
rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 31])
total number of confs: 35
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040435 none N#CC1=CC=C(C(=O)[O-])C(C=NNC(=O)C2=CC=C(F)C=C2Br)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 6, 6, 8, 8, 8, 21, 21, 20, 21, 21, 21, 21, 1, 1, 1, 6, 8, 21, 21, 21, 1] 21
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 23, 24, 25, 31] set([7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30])
total number of confs: 52
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040435 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040435
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040435/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040435
Building REAL300000040436
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040436'
/scratch/stefan/7769621/working/building/REAL300000040436 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040436

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040436/0 /scratch/stefan/7769621/working/building/REAL300000040436 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 530)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/530
`/scratch/stefan/7769621/working/3D/530' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NSC(C=NNC(=O)C2=CC=C(F)C=C2Br)=C1C(=O)[O-])

`REAL300000040436.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040436.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040436/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040436 none CC1=NSC(C=NNC(=O)C2=CC=C(F)C=C2Br)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [23, 23, 23, 23, 15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 15, 7, 1, 1, 1] 23
rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 45
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040436 none CC1=NSC(C=NNC(=O)C2=CC=C(F)C=C2Br)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 23, 23, 12, 19, 23, 23, 23, 1, 1, 3, 3, 2, 2, 2, 6, 12, 23, 23, 23] 23
rigid atoms, others: [0, 1, 2, 3, 4, 5, 18, 19] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 100
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040436 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040436
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040436/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040436
Building REAL300000040437
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040437'
/scratch/stefan/7769621/working/building/REAL300000040437 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040437

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040437/0 /scratch/stefan/7769621/working/building/REAL300000040437 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 531)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/531
`/scratch/stefan/7769621/working/3D/531' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=NNC(=O)C1=CC=C(F)C=C1Br)

`REAL300000040437.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040437.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040437/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040437 none COC1=CC(C(=O)[O-])=CC=C1C=NNC(=O)C1=CC=C(F)C=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 37, 41, 41, 41, 41, 41, 41, 15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 15, 7, 1, 1, 1] 41
rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 85
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040437 none COC1=CC(C(=O)[O-])=CC=C1C=NNC(=O)C1=CC=C(F)C=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 14, 14, 14, 41, 41, 41, 41, 41, 40, 41, 4, 4, 4, 1, 1, 1, 8, 14, 41, 41, 41] 41
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29] set([0, 32, 34, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 87
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040437 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040437
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040437/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040437
Building REAL300000040438
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040438'
/scratch/stefan/7769621/working/building/REAL300000040438 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040438

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040438/0 /scratch/stefan/7769621/working/building/REAL300000040438 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 532)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/532
`/scratch/stefan/7769621/working/3D/532' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=CC=C2OCC(=O)[O-])C(O)=C1)

`REAL300000040438.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040438.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040438/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040438 none CC1=CC=C(C(=O)NN=CC2=CC=CC=C2OCC(=O)[O-])C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
162  conformations in input
total number of sets (complete confs): 162
using faster count positions algorithm for large data
unique positions, atoms: [30, 25, 30, 30, 12, 12, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 32, 46, 46, 30, 30, 30, 30, 30, 30, 30, 30, 12, 4, 1, 1, 1, 1, 32, 32, 60, 30] 162
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])
total number of confs: 287
number of broken/clashed sets: 28
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040438 none CC1=CC=C(C(=O)NN=CC2=CC=CC=C2OCC(=O)[O-])C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
162  conformations in input
total number of sets (complete confs): 162
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 16, 16, 30, 30, 16, 30, 30, 30, 65, 81, 81, 81, 1, 1, 1, 2, 2, 2, 1, 1, 9, 16, 30, 30, 30, 30, 81, 81, 2, 1] 162
rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 21, 22, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 259
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040438 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040438
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040438/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040438
Building REAL300000040439
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040439'
/scratch/stefan/7769621/working/building/REAL300000040439 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040439

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040439/0 /scratch/stefan/7769621/working/building/REAL300000040439 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 533)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/533
`/scratch/stefan/7769621/working/3D/533' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1)

`REAL300000040439.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040439.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040439/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040439 none CC(=NNC(=O)C1=CC=C(C)C=C1O)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.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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]
1  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: [12, 1, 12, 12, 41, 41, 41, 75, 75, 69, 75, 75, 75, 75, 1, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 13, 13, 13, 41, 75, 75, 75, 75, 75, 75, 150, 12, 12, 1, 1, 12, 12] 172
rigid atoms, others: [41, 42, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44])
total number of confs: 365
number of broken/clashed sets: 28
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040439 none CC(=NNC(=O)C1=CC=C(C)C=C1O)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.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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]
1  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: [6, 1, 6, 6, 28, 28, 28, 57, 57, 46, 57, 57, 57, 57, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 6, 6, 6, 28, 57, 57, 57, 57, 57, 57, 114, 1, 1, 12, 12, 1, 1] 172
rigid atoms, others: [1, 39, 40, 43, 44, 14, 15, 16, 17, 18, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42])
total number of confs: 281
number of broken/clashed sets: 28
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040439 none CC(=NNC(=O)C1=CC=C(C)C=C1O)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.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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]
1  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: [27, 27, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 27, 57, 57, 27, 27, 75, 75, 75, 75, 75, 75, 75, 57, 57, 28, 28, 28, 10, 1, 1, 2, 2, 2, 1, 2, 57, 57, 75, 75, 57, 57] 172
rigid atoms, others: [32, 33, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 242
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040439 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040439
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040439/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040439
Building REAL300000040440
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040440'
/scratch/stefan/7769621/working/building/REAL300000040440 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040440

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040440/0 /scratch/stefan/7769621/working/building/REAL300000040440 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 534)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/534
`/scratch/stefan/7769621/working/3D/534' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)C2=CC=C(C)C=C2O)=CC=C1OCC(=O)[O-])

`REAL300000040440.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040440.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040440/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040440 none COC1=CC(C=NNC(=O)C2=CC=C(C)C=C2O)=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.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [63, 32, 32, 32, 10, 10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 129, 201, 201, 201, 63, 63, 63, 32, 10, 6, 1, 1, 2, 2, 2, 1, 2, 32, 32, 201, 201] 402
rigid atoms, others: [32, 33, 37, 8, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 604
number of broken/clashed sets: 93
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040440 none COC1=CC(C=NNC(=O)C2=CC=C(C)C=C2O)=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.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 15, 15, 14, 32, 32, 19, 32, 32, 32, 32, 1, 1, 1, 1, 9, 42, 67, 67, 4, 4, 4, 1, 7, 15, 32, 32, 32, 32, 32, 32, 64, 1, 1, 42, 42] 402
rigid atoms, others: [1, 2, 3, 4, 5, 39, 40, 18, 19, 20, 21, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42])
total number of confs: 405
number of broken/clashed sets: 93
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040440 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040440
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040440/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040440
Building REAL300000040441
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040441'
/scratch/stefan/7769621/working/building/REAL300000040441 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040441

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040441/0 /scratch/stefan/7769621/working/building/REAL300000040441 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 535)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/535
`/scratch/stefan/7769621/working/3D/535' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=C(OCC(=O)[O-])C=C2)C(O)=C1)

`REAL300000040441.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040441.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040441/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040441 none CC1=CC=C(C(=O)NN=CC2=CC=C(OCC(=O)[O-])C=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 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: [61, 40, 61, 61, 23, 23, 23, 7, 7, 1, 1, 1, 1, 1, 1, 5, 29, 45, 45, 1, 1, 61, 61, 61, 61, 61, 61, 61, 61, 23, 7, 1, 1, 29, 29, 1, 1, 122, 61] 402
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])
total number of confs: 440
number of broken/clashed sets: 125
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040441 none CC1=CC=C(C(=O)NN=CC2=CC=C(OCC(=O)[O-])C=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 10, 10, 10, 31, 31, 61, 61, 31, 31, 117, 201, 201, 201, 61, 61, 1, 1, 1, 2, 2, 2, 1, 1, 10, 31, 61, 61, 201, 201, 61, 61, 2, 1] 402
rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 21, 22, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 689
number of broken/clashed sets: 125
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040441 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040441
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040441/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040441
Building REAL300000040442
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040442'
/scratch/stefan/7769621/working/building/REAL300000040442 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040442

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040442/0 /scratch/stefan/7769621/working/building/REAL300000040442 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 536)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/536
`/scratch/stefan/7769621/working/3D/536' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=CC(OCC(=O)[O-])=C1)

`REAL300000040442.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040442.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040442/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040442 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 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]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 22, 22, 22, 60, 60, 37, 60, 60, 60, 60, 1, 1, 1, 1, 1, 1, 7, 26, 41, 41, 1, 11, 11, 11, 22, 60, 60, 60, 60, 60, 60, 120, 1, 1, 1, 26, 26, 1] 402
rigid atoms, others: [1, 36, 37, 38, 41, 14, 15, 16, 17, 18, 19, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40])
total number of confs: 444
number of broken/clashed sets: 114
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040442 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 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]
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: [19, 19, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 19, 60, 60, 60, 60, 60, 133, 201, 201, 201, 60, 19, 19, 19, 10, 1, 1, 2, 2, 2, 1, 2, 60, 60, 60, 201, 201, 60] 402
rigid atoms, others: [34, 4, 6, 7, 8, 9, 10, 11, 12, 13, 29, 30] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 545
number of broken/clashed sets: 114
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040442 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040442
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040442/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040442
Building REAL300000040443
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040443'
/scratch/stefan/7769621/working/building/REAL300000040443 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040443

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040443/0 /scratch/stefan/7769621/working/building/REAL300000040443 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 537)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/537
`/scratch/stefan/7769621/working/3D/537' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=C(C(=O)[O-])C=C1)

`REAL300000040443.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040443.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040443/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040443 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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]
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: [4, 1, 4, 4, 7, 7, 7, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 2, 2, 1, 1, 4, 4, 4, 7, 19, 19, 19, 19, 19, 19, 38, 1, 1, 1, 1] 38
rigid atoms, others: [1, 34, 35, 36, 37, 14, 15, 16, 17, 18, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 78
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040443 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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]
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: [7, 7, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 7, 19, 19, 19, 19, 19, 7, 7, 7, 6, 1, 1, 2, 2, 2, 1, 2, 19, 19, 19, 19] 38
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 33, 34, 35, 36, 37])
total number of confs: 83
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040443 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040443
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040443/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040443
Building REAL300000040444
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040444'
/scratch/stefan/7769621/working/building/REAL300000040444 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040444

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040444/0 /scratch/stefan/7769621/working/building/REAL300000040444 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 538)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/538
`/scratch/stefan/7769621/working/3D/538' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=C(CC(=O)[O-])C=C1)

`REAL300000040444.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040444.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040444/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040444 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 17, 17, 17, 31, 31, 29, 31, 31, 31, 31, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 6, 6, 6, 17, 31, 31, 31, 31, 31, 31, 62, 1, 1, 2, 2, 1, 1] 90
rigid atoms, others: [1, 35, 36, 39, 40, 14, 15, 16, 17, 18, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 153
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040444 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 18, 31, 31, 19, 31, 45, 45, 45, 31, 31, 18, 18, 18, 10, 1, 1, 2, 2, 2, 1, 2, 31, 31, 45, 45, 31, 31] 90
rigid atoms, others: [33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 200
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040444 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040444
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040444/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040444
Building REAL300000040445
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040445'
/scratch/stefan/7769621/working/building/REAL300000040445 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040445

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040445/0 /scratch/stefan/7769621/working/building/REAL300000040445 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 539)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/539
`/scratch/stefan/7769621/working/3D/539' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])OC2=C1C(=NNC(=O)C1=CC=C(C)C=C1O)CCC2)

`REAL300000040445.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040445.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040445/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040445 none CC1=C(C(=O)[O-])OC2=C1C(=NNC(=O)C1=CC=C(C)C=C1O)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.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 4, 7, 6, 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]
1  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 10, 1, 1, 2, 2, 2, 1, 2, 23, 23, 23, 23, 23, 23] 46
rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 47
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040445 none CC1=C(C(=O)[O-])OC2=C1C(=NNC(=O)C1=CC=C(C)C=C1O)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.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 4, 7, 6, 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]
1  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 23, 12, 23, 23, 23, 23, 1, 1, 1, 2, 2, 2, 7, 23, 23, 23, 23, 23, 23, 46, 1, 1, 1, 1, 1, 1] 46
rigid atoms, others: [0, 1, 2, 3, 36, 37, 6, 7, 8, 9, 10, 11, 40, 41, 22, 23, 24, 39, 38] set([4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 120
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040445 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040445
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040445/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040445
Building REAL300000040446
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040446'
/scratch/stefan/7769621/working/building/REAL300000040446 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040446

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040446/0 /scratch/stefan/7769621/working/building/REAL300000040446 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 540)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/540
`/scratch/stefan/7769621/working/3D/540' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=C(OCCC(=O)[O-])C=C2)C(O)=C1)

`REAL300000040446.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040446.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040446/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040446 none CC1=CC=C(C(=O)NN=CC2=CC=C(OCCC(=O)[O-])C=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 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]
1  hydrogens need rotated
346  conformations in input
total number of sets (complete confs): 346
using faster count positions algorithm for large data
unique positions, atoms: [42, 26, 42, 42, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 1, 6, 29, 47, 61, 55, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 15, 6, 1, 1, 29, 29, 46, 46, 1, 1, 84, 42] 346
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])
total number of confs: 443
number of broken/clashed sets: 127
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040446 none CC1=CC=C(C(=O)NN=CC2=CC=C(OCCC(=O)[O-])C=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 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]
1  hydrogens need rotated
348  conformations in input
total number of sets (complete confs): 348
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 24, 24, 43, 43, 25, 25, 92, 146, 174, 174, 174, 43, 43, 1, 1, 1, 2, 2, 2, 1, 1, 10, 24, 43, 43, 146, 146, 174, 174, 43, 43, 2, 1] 348
rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 22, 23, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 609
number of broken/clashed sets: 128
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040446 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040446
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040446/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040446
Building REAL300000040447
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040447'
/scratch/stefan/7769621/working/building/REAL300000040447 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040447

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040447/0 /scratch/stefan/7769621/working/building/REAL300000040447 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 541)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/541
`/scratch/stefan/7769621/working/3D/541' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=CC(OC(C)C(=O)[O-])=C2)C(O)=C1)

`REAL300000040447.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040447.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040447/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040447 none CC1=CC=C(C(=O)NN=CC2=CC=CC(OC(C)C(=O)[O-])=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [53, 34, 53, 53, 18, 18, 18, 9, 9, 1, 1, 1, 1, 1, 1, 1, 11, 30, 30, 42, 42, 1, 53, 53, 53, 53, 53, 53, 53, 53, 18, 9, 1, 1, 1, 30, 30, 30, 30, 1, 106, 53] 292
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])
total number of confs: 411
number of broken/clashed sets: 62
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040447 none CC1=CC=C(C(=O)NN=CC2=CC=CC(OC(C)C(=O)[O-])=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [1, 1, 1, 1, 1, 1, 11, 11, 11, 25, 25, 53, 53, 53, 53, 53, 128, 146, 146, 146, 146, 53, 1, 1, 1, 2, 2, 2, 1, 1, 11, 25, 53, 53, 53, 146, 146, 146, 146, 53, 2, 1] 292
rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 22, 23, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 303
number of broken/clashed sets: 62
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040447 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040447
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040447/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040447
Building REAL300000040448
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040448'
/scratch/stefan/7769621/working/building/REAL300000040448 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040448

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040448/0 /scratch/stefan/7769621/working/building/REAL300000040448 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 542)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/542
`/scratch/stefan/7769621/working/3D/542' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=CC(OCCC(=O)[O-])=C2)C(O)=C1)

`REAL300000040448.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040448.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040448/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040448 none CC1=CC=C(C(=O)NN=CC2=CC=CC(OCCC(=O)[O-])=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [49, 30, 49, 49, 19, 19, 19, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 26, 43, 60, 51, 1, 49, 49, 49, 49, 49, 49, 49, 49, 19, 8, 1, 1, 1, 26, 26, 43, 43, 1, 98, 49] 402
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])
total number of confs: 481
number of broken/clashed sets: 150
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040448 none CC1=CC=C(C(=O)NN=CC2=CC=CC(OCCC(=O)[O-])=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 7, 7, 7, 16, 16, 49, 49, 49, 49, 49, 126, 180, 201, 201, 199, 49, 1, 1, 1, 2, 2, 2, 1, 1, 7, 16, 49, 49, 49, 180, 180, 201, 201, 49, 2, 1] 402
rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 22, 23, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 570
number of broken/clashed sets: 150
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040448 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040448
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040448/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040448
Building REAL300000040449
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040449'
/scratch/stefan/7769621/working/building/REAL300000040449 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040449

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040449/0 /scratch/stefan/7769621/working/building/REAL300000040449 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 543)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/543
`/scratch/stefan/7769621/working/3D/543' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)C(O)=C1)

`REAL300000040449.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040449.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040449/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040449 none CC1=CC=C(C(=O)NN=CC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 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: [14, 13, 14, 14, 7, 8, 8, 7, 7, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 1, 1, 2, 2, 1, 14, 14, 14, 14, 14, 14, 14, 14, 8, 7, 1, 1, 5, 5, 1, 28, 14] 38
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])
total number of confs: 85
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040449 none CC1=CC=C(C(=O)NN=CC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 6, 14, 14, 12, 14, 19, 19, 19, 19, 14, 14, 14, 14, 14, 1, 1, 1, 2, 2, 2, 1, 1, 5, 6, 14, 14, 19, 19, 14, 2, 1] 38
rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 53
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040449 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040449
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040449/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040449
Building REAL300000040450
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040450'
/scratch/stefan/7769621/working/building/REAL300000040450 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040450

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040450/0 /scratch/stefan/7769621/working/building/REAL300000040450 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 544)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/544
`/scratch/stefan/7769621/working/3D/544' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=CC(OCC(=O)[O-])=C2)C(O)=C1)

`REAL300000040450.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040450.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040450/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040450 none CC1=CC=C(C(=O)NN=CC2=CC=CC(OCC(=O)[O-])=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [52, 30, 52, 52, 17, 17, 17, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 28, 40, 40, 1, 52, 52, 52, 52, 52, 52, 52, 52, 17, 7, 1, 1, 1, 28, 28, 1, 104, 52] 402
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])
total number of confs: 406
number of broken/clashed sets: 135
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040450 none CC1=CC=C(C(=O)NN=CC2=CC=CC(OCC(=O)[O-])=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
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, 10, 10, 10, 22, 22, 52, 52, 52, 52, 52, 131, 201, 201, 201, 52, 1, 1, 1, 2, 2, 2, 1, 1, 10, 22, 52, 52, 52, 201, 201, 52, 2, 1] 402
rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 21, 22, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 567
number of broken/clashed sets: 135
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040450 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040450
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040450/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040450
Building REAL300000040451
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040451'
/scratch/stefan/7769621/working/building/REAL300000040451 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040451

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040451/0 /scratch/stefan/7769621/working/building/REAL300000040451 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 545)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/545
`/scratch/stefan/7769621/working/3D/545' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=C(OCC3=C(C(=O)[O-])C=CO3)C=C2)C(O)=C1)

`REAL300000040451.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040451.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040451/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040451 none CC1=CC=C(C(=O)NN=CC2=CC=C(OCC3=C(C(=O)[O-])C=CO3)C=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [70, 70, 70, 70, 42, 42, 42, 32, 32, 21, 12, 21, 21, 12, 6, 1, 1, 1, 1, 3, 3, 1, 1, 1, 21, 21, 70, 70, 70, 70, 70, 70, 70, 70, 42, 32, 20, 21, 6, 6, 1, 1, 21, 21, 140, 70] 140
rigid atoms, others: [40, 41, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45])
total number of confs: 353
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: REAL300000040451 none CC1=CC=C(C(=O)NN=CC2=CC=C(OCC3=C(C(=O)[O-])C=CO3)C=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [30, 22, 30, 30, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 2, 10, 21, 21, 23, 23, 21, 21, 21, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 14, 5, 1, 1, 10, 10, 21, 21, 1, 1, 60, 30] 140
rigid atoms, others: [43, 36, 37, 9, 10, 11, 12, 13, 14, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 44, 45])
total number of confs: 204
number of broken/clashed sets: 54
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040451 none CC1=CC=C(C(=O)NN=CC2=CC=C(OCC3=C(C(=O)[O-])C=CO3)C=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 22, 22, 30, 30, 22, 22, 37, 43, 70, 70, 70, 70, 70, 70, 70, 30, 30, 1, 1, 1, 2, 2, 2, 1, 1, 10, 22, 30, 30, 43, 43, 70, 70, 30, 30, 2, 1] 140
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 45, 26, 27, 28, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 167
number of broken/clashed sets: 54
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040451 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040451
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040451/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040451
Building REAL300000040452
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040452'
/scratch/stefan/7769621/working/building/REAL300000040452 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040452

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040452/0 /scratch/stefan/7769621/working/building/REAL300000040452 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 546)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/546
`/scratch/stefan/7769621/working/3D/546' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNC(=O)C2=CC=C(C)C=C2O)C(OCC(=O)[O-])=C1)

`REAL300000040452.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040452.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040452/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040452 none COC1=CC=C(C=NNC(=O)C2=CC=C(C)C=C2O)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.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
286  conformations in input
total number of sets (complete confs): 286
using faster count positions algorithm for large data
unique positions, atoms: [52, 35, 20, 35, 35, 19, 19, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 91, 142, 143, 143, 35, 52, 52, 52, 35, 35, 19, 10, 1, 1, 2, 2, 2, 1, 2, 142, 142, 35] 286
rigid atoms, others: [33, 34, 38, 9, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 498
number of broken/clashed sets: 48
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040452 none COC1=CC=C(C=NNC(=O)C2=CC=C(C)C=C2O)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.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
286  conformations in input
total number of sets (complete confs): 286
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 35, 35, 21, 35, 35, 35, 35, 1, 1, 8, 38, 54, 54, 1, 3, 3, 3, 1, 1, 4, 10, 35, 35, 35, 35, 35, 35, 70, 38, 38, 1] 286
rigid atoms, others: [1, 2, 3, 4, 5, 6, 42, 19, 20, 25, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 356
number of broken/clashed sets: 48
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040452 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040452
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040452/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040452
Building REAL300000040453
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040453'
/scratch/stefan/7769621/working/building/REAL300000040453 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040453

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040453/0 /scratch/stefan/7769621/working/building/REAL300000040453 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 547)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/547
`/scratch/stefan/7769621/working/3D/547' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)C(O)=C1)

`REAL300000040453.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040453.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040453/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040453 none CC1=CC=C(C(=O)NN=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 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: [30, 19, 30, 30, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 1, 12, 48, 48, 48, 69, 69, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 12, 5, 1, 1, 1, 1, 60, 30] 402
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])
total number of confs: 384
number of broken/clashed sets: 85
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040453 none CC1=CC=C(C(=O)NN=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 8, 8, 8, 19, 19, 30, 30, 19, 19, 97, 201, 201, 201, 201, 201, 30, 30, 1, 1, 1, 2, 2, 2, 1, 1, 8, 19, 30, 30, 30, 30, 2, 1] 402
rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 659
number of broken/clashed sets: 85
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040453 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040453
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040453/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040453
Building REAL300000040454
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040454'
/scratch/stefan/7769621/working/building/REAL300000040454 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040454

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040454/0 /scratch/stefan/7769621/working/building/REAL300000040454 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 548)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/548
`/scratch/stefan/7769621/working/3D/548' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=C(Br)C=C(C(=O)[O-])N2C)C(O)=C1)

`REAL300000040454.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040454.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040454/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040454 none CC1=CC=C(C(=O)NN=CC2=C(Br)C=C(C(=O)[O-])N2C)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 17, 1, 1, 1, 11, 11, 8, 5, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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]
1  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [33, 33, 33, 33, 17, 17, 17, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 17, 8, 1, 2, 2, 2, 66, 33] 66
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])
total number of confs: 141
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040454 none CC1=CC=C(C(=O)NN=CC2=C(Br)C=C(C(=O)[O-])N2C)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 17, 1, 1, 1, 11, 11, 8, 5, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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]
1  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 21, 21, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 2, 2, 2, 1, 1, 9, 21, 33, 33, 33, 33, 2, 1] 66
rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 64
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040454 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040454
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040454/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040454
Building REAL300000040455
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040455'
/scratch/stefan/7769621/working/building/REAL300000040455 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040455

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040455/0 /scratch/stefan/7769621/working/building/REAL300000040455 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 549)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/549
`/scratch/stefan/7769621/working/3D/549' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC(=O)C2=CC=C(C)C=C2O)C=C1)

`REAL300000040455.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040455.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040455/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040455 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC(=O)C2=CC=C(C)C=C2O)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.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 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]
1  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 24, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 24, 9, 1, 1, 2, 2, 2, 1, 2, 30, 30] 60
rigid atoms, others: [33, 34, 38, 15, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 39, 40, 41])
total number of confs: 58
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040455 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC(=O)C2=CC=C(C)C=C2O)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.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 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]
1  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 5, 12, 12, 12, 30, 30, 20, 30, 30, 30, 30, 1, 1, 3, 3, 3, 1, 5, 12, 30, 30, 30, 30, 30, 30, 60, 1, 1] 60
rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 9, 10, 11, 12, 41, 25, 26, 30] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 173
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040455 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040455
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040455/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040455
Building REAL300000040456
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040456'
/scratch/stefan/7769621/working/building/REAL300000040456 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040456

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040456/0 /scratch/stefan/7769621/working/building/REAL300000040456 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 550)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/550
`/scratch/stefan/7769621/working/3D/550' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=C(C(=O)[O-])C=C1)

`REAL300000040456.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040456.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040456/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040456 none CCC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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]
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: [13, 7, 1, 7, 7, 23, 23, 23, 35, 35, 34, 35, 35, 35, 35, 1, 1, 1, 1, 1, 2, 2, 1, 1, 13, 13, 13, 13, 13, 23, 35, 35, 35, 35, 35, 35, 70, 1, 1, 1, 1] 86
rigid atoms, others: [2, 37, 38, 39, 40, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 187
number of broken/clashed sets: 55
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040456 none CCC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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]
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: [30, 21, 21, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 21, 35, 35, 22, 35, 35, 35, 35, 35, 30, 30, 30, 30, 30, 9, 1, 1, 2, 2, 2, 1, 2, 35, 35, 35, 35] 86
rigid atoms, others: [35, 5, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 36, 37, 38, 39, 40])
total number of confs: 173
number of broken/clashed sets: 55
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040456 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040456
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040456/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040456
Building REAL300000040457
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040457'
/scratch/stefan/7769621/working/building/REAL300000040457 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040457

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040457/0 /scratch/stefan/7769621/working/building/REAL300000040457 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 551)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/551
`/scratch/stefan/7769621/working/3D/551' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=CC=C1C(=O)[O-])

`REAL300000040457.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040457.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040457/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040457 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7]
1  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 5, 13, 13, 13, 25, 25, 24, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 13, 25, 25, 25, 25, 25, 25, 50, 1, 1, 1, 1] 50
rigid atoms, others: [1, 34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 20] set([0, 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])
total number of confs: 115
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040457 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7]
1  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: [18, 18, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 18, 25, 25, 25, 25, 25, 25, 25, 25, 18, 18, 18, 8, 1, 1, 2, 2, 2, 1, 2, 25, 25, 25, 25] 50
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 33, 34, 35, 36, 37])
total number of confs: 53
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040457 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040457
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040457/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040457
Building REAL300000040458
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040458'
/scratch/stefan/7769621/working/building/REAL300000040458 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040458

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040458/0 /scratch/stefan/7769621/working/building/REAL300000040458 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 552)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/552
`/scratch/stefan/7769621/working/3D/552' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC(C(=O)[O-])=CC=C1O)

`REAL300000040458.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040458.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040458/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040458 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 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]
2  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: [9, 1, 9, 9, 25, 25, 25, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 25, 45, 45, 45, 45, 45, 45, 90, 1, 1, 1, 2] 180
rigid atoms, others: [1, 35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38])
total number of confs: 184
number of broken/clashed sets: 32
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040458 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 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]
2  hydrogens need rotated
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 24, 45, 45, 45, 45, 45, 45, 45, 45, 45, 24, 24, 24, 10, 1, 1, 2, 2, 2, 1, 2, 45, 45, 45, 88] 180
rigid atoms, others: [33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 171
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040458 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040458
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040458/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040458
Building REAL300000040459
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040459'
/scratch/stefan/7769621/working/building/REAL300000040459 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040459

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040459/0 /scratch/stefan/7769621/working/building/REAL300000040459 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 553)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/553
`/scratch/stefan/7769621/working/3D/553' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC(C(=O)[O-])=CC=C1F)

`REAL300000040459.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040459.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040459/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040459 none CCC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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]
1  hydrogens need rotated
152  conformations in input
total number of sets (complete confs): 152
using faster count positions algorithm for large data
unique positions, atoms: [23, 11, 1, 11, 11, 33, 33, 33, 72, 72, 63, 72, 72, 72, 72, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 23, 23, 23, 23, 23, 33, 72, 72, 72, 72, 72, 72, 144, 1, 1, 1] 152
rigid atoms, others: [2, 38, 39, 40, 15, 16, 17, 18, 21, 22, 23, 24] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 399
number of broken/clashed sets: 95
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040459 none CCC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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]
1  hydrogens need rotated
152  conformations in input
total number of sets (complete confs): 152
using faster count positions algorithm for large data
unique positions, atoms: [44, 29, 29, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 29, 72, 72, 72, 72, 72, 72, 72, 72, 72, 44, 44, 44, 44, 44, 10, 1, 1, 2, 2, 2, 1, 2, 72, 72, 72] 152
rigid atoms, others: [32, 36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 204
number of broken/clashed sets: 95
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040459 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040459
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040459/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040459
Building REAL300000040460
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040460'
/scratch/stefan/7769621/working/building/REAL300000040460 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040460

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040460/0 /scratch/stefan/7769621/working/building/REAL300000040460 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 554)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/554
`/scratch/stefan/7769621/working/3D/554' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=C3C=CC(C(=O)[O-])=CC3=NN2)C(O)=C1)

`REAL300000040460.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040460.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040460/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040460 none CC1=CC=C(C(=O)NN=CC2=C3C=CC(C(=O)[O-])=CC3=NN2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [18, 18, 18, 18, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 10, 5, 1, 1, 1, 1, 36, 18] 36
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, 36, 37, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 72
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040460 none CC1=CC=C(C(=O)NN=CC2=C3C=CC(C(=O)[O-])=CC3=NN2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 2, 2, 2, 1, 1, 9, 16, 18, 18, 18, 18, 2, 1] 36
rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 23, 24, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 40
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040460 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040460/1 /scratch/stefan/7769621/working/building/REAL300000040460 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 555)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/555
`/scratch/stefan/7769621/working/3D/555' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=NNC3=CC(C(=O)[O-])=CC=C23)C(O)=C1)

`REAL300000040460.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040460.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040460/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040460 none CC1=CC=C(C(=O)NN=CC2=NNC3=CC(C(=O)[O-])=CC=C23)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 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]
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, 35, 35, 35, 18, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 18, 6, 1, 1, 1, 1, 70, 35] 70
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])
total number of confs: 146
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040460 none CC1=CC=C(C(=O)NN=CC2=NNC3=CC(C(=O)[O-])=CC=C23)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 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]
1  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 19, 19, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 2, 2, 2, 1, 1, 8, 19, 35, 35, 35, 35, 2, 1] 70
rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 23, 24, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 73
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040460 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040460
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040460/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040460/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040460
Building REAL300000040461
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040461'
/scratch/stefan/7769621/working/building/REAL300000040461 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040461

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040461/0 /scratch/stefan/7769621/working/building/REAL300000040461 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 556)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/556
`/scratch/stefan/7769621/working/3D/556' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=CC(C(=O)[O-])=C1)

`REAL300000040461.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040461.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040461/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040461 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7]
1  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 15, 15, 15, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 2, 2, 1, 9, 9, 9, 15, 30, 30, 30, 30, 30, 30, 60, 1, 1, 1, 1] 60
rigid atoms, others: [1, 34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 128
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040461 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7]
1  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 19, 30, 30, 30, 30, 30, 30, 30, 30, 19, 19, 19, 9, 1, 1, 2, 2, 2, 1, 2, 30, 30, 30, 30] 60
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 33, 34, 35, 36, 37])
total number of confs: 61
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040461 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040461
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040461/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040461
Building REAL300000040462
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040462'
/scratch/stefan/7769621/working/building/REAL300000040462 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040462

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040462/0 /scratch/stefan/7769621/working/building/REAL300000040462 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 557)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/557
`/scratch/stefan/7769621/working/3D/557' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CN(CC(=O)[O-])N=N2)C(O)=C1)

`REAL300000040462.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040462.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040462/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040462 none CC1=CC=C(C(=O)NN=CC2=CN(CC(=O)[O-])N=N2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 8, 8, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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]
1  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [37, 25, 37, 37, 17, 17, 17, 7, 7, 1, 1, 1, 1, 1, 8, 17, 17, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 16, 7, 1, 8, 8, 74, 37] 114
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])
total number of confs: 244
number of broken/clashed sets: 24
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040462 none CC1=CC=C(C(=O)NN=CC2=CN(CC(=O)[O-])N=N2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 8, 8, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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]
1  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 26, 26, 37, 37, 37, 57, 57, 57, 37, 37, 1, 1, 1, 2, 2, 2, 1, 1, 9, 26, 37, 57, 57, 2, 1] 114
rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32])
total number of confs: 166
number of broken/clashed sets: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040462 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040462
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040462/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040462
Building REAL300000040463
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040463'
/scratch/stefan/7769621/working/building/REAL300000040463 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040463

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040463/0 /scratch/stefan/7769621/working/building/REAL300000040463 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 558)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/558
`/scratch/stefan/7769621/working/3D/558' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=C(C(=O)[O-])C(F)=C1)

`REAL300000040463.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040463.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040463/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040463 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 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]
1  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 35, 35, 35, 58, 58, 58, 58, 58, 58, 58, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 11, 11, 11, 35, 58, 58, 58, 58, 58, 58, 116, 1, 1, 1] 116
rigid atoms, others: [1, 35, 36, 37, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 248
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040463 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 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]
1  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [23, 23, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 23, 58, 58, 58, 58, 58, 58, 58, 58, 58, 23, 23, 23, 10, 1, 1, 2, 2, 2, 1, 2, 58, 58, 58] 116
rigid atoms, others: [33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 99
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040463 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040463
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040463/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040463
Building REAL300000040464
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040464'
/scratch/stefan/7769621/working/building/REAL300000040464 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040464

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040464/0 /scratch/stefan/7769621/working/building/REAL300000040464 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 559)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/559
`/scratch/stefan/7769621/working/3D/559' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC(C(=O)[O-])=CS2)C(O)=C1)

`REAL300000040464.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040464.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040464/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040464 none CC1=CC=C(C(=O)NN=CC2=CC(C(=O)[O-])=CS2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [33, 32, 33, 33, 18, 18, 18, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 17, 8, 1, 1, 66, 33] 66
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])
total number of confs: 140
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040464 none CC1=CC=C(C(=O)NN=CC2=CC(C(=O)[O-])=CS2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 22, 22, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 2, 2, 2, 1, 1, 10, 22, 33, 33, 2, 1] 66
rigid atoms, others: [0, 1, 2, 3, 4, 5, 18, 19, 20, 24, 25, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30])
total number of confs: 65
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040464 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040464
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040464/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040464
Building REAL300000040465
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040465'
/scratch/stefan/7769621/working/building/REAL300000040465 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040465

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040465/0 /scratch/stefan/7769621/working/building/REAL300000040465 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 560)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/560
`/scratch/stefan/7769621/working/3D/560' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)C2=CC=C(C)C=C2O)=CC=C1OCCC(=O)[O-])

`REAL300000040465.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040465.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040465/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040465 none COC1=CC(C=NNC(=O)C2=CC=C(C)C=C2O)=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.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 25, 25, 25, 9, 9, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 96, 182, 194, 201, 193, 50, 50, 50, 25, 9, 6, 1, 1, 2, 2, 2, 1, 2, 25, 25, 182, 182, 194, 194] 402
rigid atoms, others: [33, 34, 38, 8, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 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: 678
number of broken/clashed sets: 115
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040465 none COC1=CC(C=NNC(=O)C2=CC=C(C)C=C2O)=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.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 11, 11, 10, 25, 25, 14, 25, 25, 25, 25, 1, 1, 1, 1, 9, 43, 59, 85, 77, 4, 4, 4, 1, 7, 11, 25, 25, 25, 25, 25, 25, 50, 1, 1, 43, 43, 58, 58] 402
rigid atoms, others: [1, 2, 3, 4, 5, 40, 41, 18, 19, 20, 21, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45])
total number of confs: 464
number of broken/clashed sets: 115
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040465 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040465
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040465/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040465
Building REAL300000040466
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040466'
/scratch/stefan/7769621/working/building/REAL300000040466 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040466

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040466/0 /scratch/stefan/7769621/working/building/REAL300000040466 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 561)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/561
`/scratch/stefan/7769621/working/3D/561' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=C(C(=O)[O-])C=C2Cl)C(O)=C1)

`REAL300000040466.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040466.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040466/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040466 none CC1=CC=C(C(=O)NN=CC2=CC=C(C(=O)[O-])C=C2Cl)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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]
1  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: [20, 20, 20, 20, 13, 13, 13, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 13, 6, 1, 1, 1, 40, 20] 40
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])
total number of confs: 91
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040466 none CC1=CC=C(C(=O)NN=CC2=CC=C(C(=O)[O-])C=C2Cl)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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]
1  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 16, 16, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 2, 2, 2, 1, 1, 7, 16, 20, 20, 20, 2, 1] 40
rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 43
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040466 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040466
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040466/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040466
Building REAL300000040467
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040467'
/scratch/stefan/7769621/working/building/REAL300000040467 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040467

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040467/0 /scratch/stefan/7769621/working/building/REAL300000040467 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 562)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/562
`/scratch/stefan/7769621/working/3D/562' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC(C(=O)[O-])=C(C)N=C1C)

`REAL300000040467.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040467.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040467/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040467 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC(C(=O)[O-])=C(C)N=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 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]
1  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 21, 21, 21, 58, 58, 48, 58, 58, 58, 58, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 9, 9, 9, 21, 58, 58, 58, 58, 58, 58, 116, 1, 2, 2, 2, 2, 2, 2] 116
rigid atoms, others: [1, 36, 14, 15, 16, 17, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42])
total number of confs: 285
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040467 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC(C(=O)[O-])=C(C)N=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 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]
1  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 29, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 30, 30, 30, 10, 1, 1, 2, 2, 2, 1, 2, 58, 58, 58, 58, 58, 58, 58] 116
rigid atoms, others: [34, 4, 6, 7, 8, 9, 10, 11, 12, 13, 29, 30] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 110
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040467 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040467
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040467/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040467
Building REAL300000040468
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040468'
/scratch/stefan/7769621/working/building/REAL300000040468 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040468

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040468/0 /scratch/stefan/7769621/working/building/REAL300000040468 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 563)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/563
`/scratch/stefan/7769621/working/3D/563' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=C(O)C(C(=O)[O-])=C2)C(O)=C1)

`REAL300000040468.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040468.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040468/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040468 none CC1=CC=C(C(=O)NN=CC2=CC=C(O)C(C(=O)[O-])=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [20, 20, 20, 20, 12, 12, 12, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 20, 20, 20, 20, 20, 20, 20, 20, 12, 8, 1, 1, 2, 1, 40, 20] 80
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])
total number of confs: 88
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040468 none CC1=CC=C(C(=O)NN=CC2=CC=C(O)C(C(=O)[O-])=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 14, 14, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 2, 2, 2, 1, 1, 8, 14, 20, 20, 40, 20, 2, 1] 80
rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 82
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040468 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040468
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040468/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040468
Building REAL300000040469
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040469'
/scratch/stefan/7769621/working/building/REAL300000040469 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040469

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040469/0 /scratch/stefan/7769621/working/building/REAL300000040469 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 564)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/564
`/scratch/stefan/7769621/working/3D/564' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC(C(=O)[O-])=CC=C1C)

`REAL300000040469.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040469.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040469/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040469 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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]
1  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: [8, 1, 8, 8, 15, 15, 15, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 8, 8, 15, 28, 28, 28, 28, 28, 28, 56, 1, 1, 1, 2, 2, 2] 56
rigid atoms, others: [1, 35, 36, 37, 14, 15, 16, 17, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40])
total number of confs: 129
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040469 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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]
1  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: [20, 20, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 20, 28, 28, 28, 28, 28, 28, 28, 28, 28, 20, 20, 20, 10, 1, 1, 2, 2, 2, 1, 2, 28, 28, 28, 28, 28, 28] 56
rigid atoms, others: [33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 62
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040469 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040469
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040469/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040469
Building REAL300000040470
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040470'
/scratch/stefan/7769621/working/building/REAL300000040470 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040470

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040470/0 /scratch/stefan/7769621/working/building/REAL300000040470 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 565)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/565
`/scratch/stefan/7769621/working/3D/565' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=C(C(=O)[O-])O1)

`REAL300000040470.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040470.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040470/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040470 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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]
1  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [6, 1, 6, 6, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 9, 15, 15, 15, 15, 15, 15, 30, 1, 1] 30
rigid atoms, others: [1, 34, 33, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 62
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040470 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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]
1  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [13, 13, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 13, 15, 15, 15, 15, 15, 15, 15, 13, 13, 13, 9, 1, 1, 2, 2, 2, 1, 2, 15, 15] 30
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 32, 33, 34])
total number of confs: 37
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040470 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040470
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040470/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040470
Building REAL300000040471
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040471'
/scratch/stefan/7769621/working/building/REAL300000040471 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040471

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040471/0 /scratch/stefan/7769621/working/building/REAL300000040471 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 566)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/566
`/scratch/stefan/7769621/working/3D/566' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=C(OC(C)C(=O)[O-])C=C2)C(O)=C1)

`REAL300000040471.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040471.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040471/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040471 none CC1=CC=C(C(=O)NN=CC2=CC=C(OC(C)C(=O)[O-])C=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 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]
1  hydrogens need rotated
358  conformations in input
total number of sets (complete confs): 358
using faster count positions algorithm for large data
unique positions, atoms: [60, 33, 60, 60, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 11, 33, 33, 45, 45, 1, 1, 60, 60, 60, 60, 60, 60, 60, 60, 20, 7, 1, 1, 33, 33, 33, 33, 1, 1, 120, 60] 358
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])
total number of confs: 460
number of broken/clashed sets: 74
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040471 none CC1=CC=C(C(=O)NN=CC2=CC=C(OC(C)C(=O)[O-])C=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 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]
1  hydrogens need rotated
358  conformations in input
total number of sets (complete confs): 358
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 29, 29, 60, 60, 30, 30, 137, 179, 179, 179, 179, 60, 60, 1, 1, 1, 2, 2, 2, 1, 1, 10, 30, 60, 60, 179, 179, 179, 179, 60, 60, 2, 1] 358
rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 22, 23, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 528
number of broken/clashed sets: 74
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040471 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040471
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040471/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040471
Building REAL300000040472
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040472'
/scratch/stefan/7769621/working/building/REAL300000040472 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040472

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040472/0 /scratch/stefan/7769621/working/building/REAL300000040472 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 567)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/567
`/scratch/stefan/7769621/working/3D/567' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=C2CCC(C(=O)[O-])C3=CC=CC=C32)C(O)=C1)

`REAL300000040472.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040472.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040472/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040472 none CC1=CC=C(C(=O)NN=C2CCC(C(=O)[O-])C3=CC=CC=C32)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.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.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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]
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: [14, 14, 14, 14, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 14] 28
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 40, 41, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 59
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040472 none CC1=CC=C(C(=O)NN=C2CCC(C(=O)[O-])C3=CC=CC=C32)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.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.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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]
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: [1, 1, 1, 1, 1, 1, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 2, 2, 2, 1, 1, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 1] 28
rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 22, 23, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 35
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040472 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040472
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040472/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040472
Building REAL300000040473
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040473'
/scratch/stefan/7769621/working/building/REAL300000040473 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040473

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040473/0 /scratch/stefan/7769621/working/building/REAL300000040473 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 568)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/568
`/scratch/stefan/7769621/working/3D/568' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CN(CC(=O)[O-])C3=CC=CC=C23)C(O)=C1)

`REAL300000040473.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040473.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040473/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040473 none CC1=CC=C(C(=O)NN=CC2=CN(CC(=O)[O-])C3=CC=CC=C23)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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]
1  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: [59, 47, 59, 59, 29, 29, 29, 6, 6, 1, 1, 1, 1, 1, 7, 11, 11, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59, 59, 29, 6, 1, 7, 7, 1, 1, 1, 1, 118, 59] 196
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])
total number of confs: 329
number of broken/clashed sets: 46
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040473 none CC1=CC=C(C(=O)NN=CC2=CN(CC(=O)[O-])C3=CC=CC=C23)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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]
1  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: [1, 1, 1, 1, 1, 1, 8, 8, 8, 26, 26, 59, 59, 59, 98, 98, 98, 59, 59, 59, 59, 59, 59, 1, 1, 1, 2, 2, 2, 1, 1, 8, 26, 59, 98, 98, 59, 59, 59, 59, 2, 1] 196
rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 291
number of broken/clashed sets: 46
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040473 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040473
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040473/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040473
Building REAL300000040474
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040474'
/scratch/stefan/7769621/working/building/REAL300000040474 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040474

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040474/0 /scratch/stefan/7769621/working/building/REAL300000040474 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 569)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/569
`/scratch/stefan/7769621/working/3D/569' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])C=C(C=NNC(=O)C2=CC=C(C)C=C2O)N1)

`REAL300000040474.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040474.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040474/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040474 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)C2=CC=C(C)C=C2O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 15, 15, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 15, 9, 1, 1, 2, 2, 2, 1, 2, 24] 48
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 34, 35])
total number of confs: 49
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040474 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)C2=CC=C(C)C=C2O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 4, 4, 9, 10, 9, 24, 24, 23, 24, 24, 24, 24, 1, 2, 2, 2, 1, 4, 9, 24, 24, 24, 24, 24, 24, 47, 1] 48
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 35, 21, 25] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 108
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040474 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040474
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040474/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040474
Building REAL300000040475
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040475'
/scratch/stefan/7769621/working/building/REAL300000040475 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040475

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040475/0 /scratch/stefan/7769621/working/building/REAL300000040475 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 570)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/570
`/scratch/stefan/7769621/working/3D/570' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=CC(OCCCC(=O)[O-])=C1)

`REAL300000040475.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040475.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040475/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040475 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 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, 6, 7, 7, 7, 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, 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: [10, 1, 10, 10, 15, 15, 15, 25, 25, 21, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 6, 25, 39, 68, 84, 84, 1, 10, 10, 10, 15, 25, 25, 25, 25, 25, 25, 50, 1, 1, 1, 25, 25, 39, 39, 69, 69, 1] 402
rigid atoms, others: [1, 38, 39, 40, 14, 15, 16, 17, 18, 19, 26, 47] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46])
total number of confs: 489
number of broken/clashed sets: 172
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040475 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 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, 6, 7, 7, 7, 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, 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: [8, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 25, 25, 25, 25, 25, 73, 127, 157, 201, 201, 201, 25, 8, 8, 8, 5, 1, 1, 2, 2, 2, 1, 2, 25, 25, 25, 127, 127, 157, 157, 201, 201, 25] 402
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 11, 12, 13, 36, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 745
number of broken/clashed sets: 172
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040475 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040475
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040475/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040475
Building REAL300000040476
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040476'
/scratch/stefan/7769621/working/building/REAL300000040476 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040476

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040476/0 /scratch/stefan/7769621/working/building/REAL300000040476 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 571)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/571
`/scratch/stefan/7769621/working/3D/571' -> `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)=NNC(=O)C1=CC=C(C)C=C1O)

`REAL300000040476.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040476.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040476/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040476 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)=NNC(=O)C1=CC=C(C)C=C1O 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', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 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]
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: [25, 25, 25, 62, 68, 68, 68, 68, 68, 174, 201, 201, 201, 201, 68, 68, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 62, 62, 68, 68, 68, 68, 201, 201, 201, 201, 68, 68, 7, 1, 1, 2, 2, 2, 1, 2] 402
rigid atoms, others: [44, 45, 49, 18, 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, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 50])
total number of confs: 542
number of broken/clashed sets: 364
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040476 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)=NNC(=O)C1=CC=C(C)C=C1O 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', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 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]
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, 4, 2, 1, 1, 1, 1, 1, 1, 11, 25, 25, 35, 35, 1, 1, 12, 12, 31, 31, 31, 68, 68, 49, 68, 68, 68, 68, 12, 12, 12, 4, 4, 2, 2, 1, 1, 25, 25, 25, 25, 1, 1, 31, 68, 68, 68, 68, 68, 68, 136] 402
rigid atoms, others: [35, 4, 5, 6, 7, 8, 41, 42, 14, 15, 3, 36] 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, 33, 34, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 468
number of broken/clashed sets: 364
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040476 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040476
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040476/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040476
Building REAL300000040477
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040477'
/scratch/stefan/7769621/working/building/REAL300000040477 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040477

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040477/0 /scratch/stefan/7769621/working/building/REAL300000040477 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 572)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/572
`/scratch/stefan/7769621/working/3D/572' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CC=C(OCC(=O)[O-])C=C1)=NNC(=O)C1=CC=C(C)C=C1O)

`REAL300000040477.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040477.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040477/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040477 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)=NNC(=O)C1=CC=C(C)C=C1O 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', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 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]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 53, 55, 55, 55, 55, 55, 133, 201, 201, 201, 55, 55, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 53, 53, 55, 55, 55, 55, 201, 201, 55, 55, 7, 1, 1, 2, 2, 2, 1, 2] 402
rigid atoms, others: [41, 42, 46, 17, 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, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 47])
total number of confs: 636
number of broken/clashed sets: 365
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040477 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)=NNC(=O)C1=CC=C(C)C=C1O 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', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 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]
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, 4, 2, 1, 1, 1, 1, 1, 1, 6, 20, 33, 33, 1, 1, 12, 12, 27, 27, 27, 55, 55, 41, 55, 55, 55, 55, 12, 12, 12, 4, 4, 2, 2, 1, 1, 20, 21, 1, 1, 27, 55, 55, 55, 55, 55, 55, 110] 402
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 39, 13, 14, 35, 38] 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, 32, 33, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 388
number of broken/clashed sets: 365
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040477 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040477
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040477/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040477
Building REAL300000040478
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040478'
/scratch/stefan/7769621/working/building/REAL300000040478 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040478

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040478/0 /scratch/stefan/7769621/working/building/REAL300000040478 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 573)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/573
`/scratch/stefan/7769621/working/3D/573' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=CC(OC(C)C(=O)[O-])=C1)

`REAL300000040478.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040478.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040478/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040478 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 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]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 22, 22, 22, 63, 63, 41, 63, 63, 63, 63, 1, 1, 1, 1, 1, 1, 11, 28, 28, 42, 42, 1, 11, 11, 11, 22, 63, 63, 63, 63, 63, 63, 126, 1, 1, 1, 28, 28, 28, 28, 1] 402
rigid atoms, others: [1, 37, 38, 39, 44, 14, 15, 16, 17, 18, 19, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43])
total number of confs: 461
number of broken/clashed sets: 86
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040478 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 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]
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: [21, 21, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 21, 63, 63, 63, 63, 63, 173, 201, 201, 201, 201, 63, 21, 21, 21, 10, 1, 1, 2, 2, 2, 1, 2, 63, 63, 63, 201, 201, 201, 201, 63] 402
rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 421
number of broken/clashed sets: 86
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040478 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040478
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040478/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040478
Building REAL300000040479
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040479'
/scratch/stefan/7769621/working/building/REAL300000040479 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040479

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040479/0 /scratch/stefan/7769621/working/building/REAL300000040479 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 574)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/574
`/scratch/stefan/7769621/working/3D/574' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)=NNC(=O)C1=CC=C(C)C=C1O)

`REAL300000040479.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040479.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040479/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040479 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)=NNC(=O)C1=CC=C(C)C=C1O 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', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 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]
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: [18, 18, 18, 53, 55, 55, 55, 55, 55, 178, 195, 201, 201, 198, 55, 55, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 53, 53, 55, 55, 55, 55, 195, 195, 201, 201, 55, 55, 6, 1, 1, 2, 2, 2, 1, 2] 402
rigid atoms, others: [44, 45, 49, 18, 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, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 50])
total number of confs: 499
number of broken/clashed sets: 362
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040479 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)=NNC(=O)C1=CC=C(C)C=C1O 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', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 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]
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: [14, 4, 2, 1, 1, 1, 1, 1, 1, 6, 16, 19, 28, 26, 1, 1, 14, 14, 34, 34, 34, 55, 55, 46, 55, 55, 55, 55, 14, 14, 14, 4, 4, 2, 2, 1, 1, 16, 17, 18, 18, 1, 1, 34, 55, 55, 55, 55, 55, 55, 110] 402
rigid atoms, others: [35, 4, 5, 6, 7, 8, 41, 42, 14, 15, 3, 36] 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, 33, 34, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 375
number of broken/clashed sets: 362
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040479 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040479
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040479/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040479
Building REAL300000040480
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040480'
/scratch/stefan/7769621/working/building/REAL300000040480 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040480

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040480/0 /scratch/stefan/7769621/working/building/REAL300000040480 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 575)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/575
`/scratch/stefan/7769621/working/3D/575' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=C(OCCCCC(=O)[O-])C=C1)

`REAL300000040480.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040480.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040480/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040480 none CCC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.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']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 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: [10, 7, 1, 7, 7, 13, 13, 13, 23, 23, 19, 23, 23, 23, 23, 1, 1, 1, 1, 1, 6, 11, 27, 36, 62, 73, 75, 1, 1, 10, 10, 10, 10, 10, 13, 23, 23, 23, 23, 23, 23, 46, 1, 1, 11, 11, 26, 26, 36, 36, 61, 61, 1, 1] 402
rigid atoms, others: [2, 42, 43, 15, 16, 17, 18, 19, 52, 53, 27, 28] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 459
number of broken/clashed sets: 375
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040480 none CCC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.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']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 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: [15, 10, 10, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 10, 23, 23, 10, 10, 53, 77, 121, 137, 179, 198, 199, 23, 23, 15, 15, 15, 15, 15, 5, 1, 1, 2, 2, 2, 1, 2, 23, 23, 70, 70, 121, 121, 137, 137, 179, 179, 23, 23] 402
rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 40] 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, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 832
number of broken/clashed sets: 375
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040480 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040480
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040480/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040480
Building REAL300000040481
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040481'
/scratch/stefan/7769621/working/building/REAL300000040481 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040481

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040481/0 /scratch/stefan/7769621/working/building/REAL300000040481 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 576)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/576
`/scratch/stefan/7769621/working/3D/576' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CSC(C(=O)[O-])=C1)

`REAL300000040481.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040481.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040481/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040481 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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]
1  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 10, 10, 21, 21, 21, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 2, 2, 1, 10, 10, 10, 21, 33, 33, 33, 33, 33, 33, 66, 1, 1] 66
rigid atoms, others: [1, 34, 33, 14, 15, 16, 17, 18, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 147
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040481 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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]
1  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 19, 33, 33, 33, 33, 33, 33, 33, 19, 19, 19, 9, 1, 1, 2, 2, 2, 1, 2, 33, 33] 66
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 32, 33, 34])
total number of confs: 65
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040481 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040481
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040481/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040481
Building REAL300000040482
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040482'
/scratch/stefan/7769621/working/building/REAL300000040482 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040482

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040482/0 /scratch/stefan/7769621/working/building/REAL300000040482 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 577)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/577
`/scratch/stefan/7769621/working/3D/577' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=C2CC(C(=O)[O-])(C3=CC=CC=C3)C2)C(O)=C1)

`REAL300000040482.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040482.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040482/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040482 none CC1=CC=C(C(=O)NN=C2CC(C(=O)[O-])(C3=CC=CC=C3)C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 18, 29, 29, 11, 11, 11, 5, 5, 5, 5, 1, 5, 7, 7, 1, 1, 1, 1, 1, 1, 5, 29, 29, 29, 29, 29, 29, 29, 29, 11, 5, 5, 1, 1, 1, 1, 1, 5, 5, 58, 29] 58
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])
total number of confs: 153
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040482 none CC1=CC=C(C(=O)NN=C2CC(C(=O)[O-])(C3=CC=CC=C3)C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 12, 24, 24, 5, 5, 5, 1, 1, 1, 1, 1, 1, 3, 3, 1, 5, 5, 1, 5, 5, 1, 24, 24, 24, 24, 24, 24, 24, 24, 5, 1, 1, 5, 5, 1, 5, 5, 1, 1, 48, 24] 58
rigid atoms, others: [32, 38, 7, 8, 9, 10, 11, 12, 15, 21, 39, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 40, 41])
total number of confs: 146
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040482 none CC1=CC=C(C(=O)NN=C2CC(C(=O)[O-])(C3=CC=CC=C3)C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 10, 10, 10, 24, 24, 24, 24, 29, 29, 24, 29, 29, 24, 29, 29, 24, 1, 1, 1, 2, 2, 2, 1, 1, 10, 24, 24, 29, 29, 24, 29, 29, 24, 24, 2, 1] 58
rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 22, 23, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 95
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040482 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040482
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040482/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040482
Building REAL300000040483
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040483'
/scratch/stefan/7769621/working/building/REAL300000040483 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040483

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040483/0 /scratch/stefan/7769621/working/building/REAL300000040483 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 578)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/578
`/scratch/stefan/7769621/working/3D/578' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(C)C=C1O)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C)

`REAL300000040483.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040483.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040483/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040483 none CC(=NNC(=O)C1=CC=C(C)C=C1O)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', '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, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 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, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 16, 16, 16, 28, 28, 25, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 5, 5, 5, 16, 28, 28, 28, 28, 28, 28, 56, 1, 1, 5, 5, 2, 2, 2, 2, 2, 2] 66
rigid atoms, others: [1, 37, 38, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 164
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040483 none CC(=NNC(=O)C1=CC=C(C)C=C1O)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', '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, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 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, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 17, 28, 28, 28, 28, 28, 33, 33, 33, 28, 28, 28, 17, 17, 17, 9, 1, 1, 2, 2, 2, 1, 2, 28, 28, 33, 33, 28, 28, 28, 28, 28, 28] 66
rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 108
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040483 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040483
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040483/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040483
Building REAL300000040484
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040484'
/scratch/stefan/7769621/working/building/REAL300000040484 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040484

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040484/0 /scratch/stefan/7769621/working/building/REAL300000040484 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 579)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/579
`/scratch/stefan/7769621/working/3D/579' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCCCCCC(=O)[O-])=NNC(=O)C1=CC=C(C)C=C1O)

`REAL300000040484.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040484.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040484/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040484 none CC(CCCCCCC(=O)[O-])=NNC(=O)C1=CC=C(C)C=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 1, 5, 5, 5, 5, 5, 5, 1, 11, 11, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 6, 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]
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: [17, 17, 17, 58, 61, 91, 108, 140, 198, 199, 199, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 58, 58, 74, 74, 89, 89, 128, 128, 151, 150, 199, 200, 5, 1, 1, 2, 2, 2, 1, 2] 402
rigid atoms, others: [39, 40, 44, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 45])
total number of confs: 1180
number of broken/clashed sets: 374
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040484 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040484
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040484/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040484
Building REAL300000040485
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040485'
/scratch/stefan/7769621/working/building/REAL300000040485 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040485

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040485/0 /scratch/stefan/7769621/working/building/REAL300000040485 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 580)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/580
`/scratch/stefan/7769621/working/3D/580' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=C2CCC(CC(=O)[O-])C2C)C(O)=C1)

`REAL300000040485.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040485.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040485/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040485 none CC1=CC=C(C(=O)NN=C2CCC(CC(=O)[O-])C2C)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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]
1  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: [16, 14, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 7, 7, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 1, 4, 4, 1, 2, 2, 2, 32, 16] 36
rigid atoms, others: [32, 35, 7, 8, 9, 10, 11, 12, 13, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 36, 37, 38, 39, 40])
total number of confs: 95
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040485 none CC1=CC=C(C(=O)NN=C2CCC(CC(=O)[O-])C2C)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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]
1  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 16, 16, 16, 16, 16, 18, 18, 18, 16, 16, 1, 1, 1, 2, 2, 2, 1, 1, 9, 16, 16, 16, 16, 16, 18, 18, 16, 16, 16, 16, 2, 1] 36
rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 50
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040485 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040485
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040485/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040485
Building REAL300000040486
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040486'
/scratch/stefan/7769621/working/building/REAL300000040486 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040486

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040486/0 /scratch/stefan/7769621/working/building/REAL300000040486 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 581)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/581
`/scratch/stefan/7769621/working/3D/581' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC(C(=O)[O-])=CS1)

`REAL300000040486.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040486.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040486/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040486 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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]
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: [10, 1, 10, 10, 21, 21, 21, 43, 43, 41, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 20, 43, 43, 43, 43, 43, 43, 86, 1, 1] 86
rigid atoms, others: [1, 34, 33, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 186
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040486 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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]
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: [22, 22, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 22, 43, 43, 43, 43, 43, 43, 43, 23, 23, 23, 10, 1, 1, 2, 2, 2, 1, 2, 43, 43] 86
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 32, 33, 34])
total number of confs: 84
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040486 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040486
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040486/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040486
Building REAL300000040487
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040487'
/scratch/stefan/7769621/working/building/REAL300000040487 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040487

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040487/0 /scratch/stefan/7769621/working/building/REAL300000040487 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 582)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/582
`/scratch/stefan/7769621/working/3D/582' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=C2CCC(C(=O)[O-])C(C)(C)C2C)C(O)=C1)

`REAL300000040487.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040487.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040487/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040487 none CC1=CC=C(C(=O)NN=C2CCC(C(=O)[O-])C(C)(C)C2C)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.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, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 5, 1, 11, 11, 5, 5, 5, 5, 5, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 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]
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: [14, 14, 14, 14, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 28, 14] 28
rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 41, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38, 39, 40, 42, 43, 44, 45, 46])
total number of confs: 71
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040487 none CC1=CC=C(C(=O)NN=C2CCC(C(=O)[O-])C(C)(C)C2C)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.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, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 5, 1, 11, 11, 5, 5, 5, 5, 5, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 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]
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: [1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 2, 2, 2, 1, 1, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 1] 28
rigid atoms, others: [0, 1, 2, 3, 4, 5, 46, 21, 22, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 34
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040487 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040487
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040487/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040487
Building REAL300000040488
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040488'
/scratch/stefan/7769621/working/building/REAL300000040488 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040488

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040488/0 /scratch/stefan/7769621/working/building/REAL300000040488 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 583)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/583
`/scratch/stefan/7769621/working/3D/583' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=C2CCC(C(=O)[O-])CC2C)C(O)=C1)

`REAL300000040488.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040488.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040488/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040488 none CC1=CC=C(C(=O)NN=C2CCC(C(=O)[O-])CC2C)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 5, 1, 11, 11, 5, 5, 5, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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]
1  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: [28, 22, 28, 28, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 8, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 56, 28] 56
rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 36, 37, 38, 39, 40])
total number of confs: 141
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040488 none CC1=CC=C(C(=O)NN=C2CCC(C(=O)[O-])CC2C)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 5, 1, 11, 11, 5, 5, 5, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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]
1  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 2, 2, 2, 1, 1, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 2, 1] 56
rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 51
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040488 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040488
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040488/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040488
Building REAL300000040489
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040489'
/scratch/stefan/7769621/working/building/REAL300000040489 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040489

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040489/0 /scratch/stefan/7769621/working/building/REAL300000040489 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 584)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/584
`/scratch/stefan/7769621/working/3D/584' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=C2CCC(C(=O)[O-])C(C)C2)C(O)=C1)

`REAL300000040489.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040489.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040489/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040489 none CC1=CC=C(C(=O)NN=C2CCC(C(=O)[O-])C(C)C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 5, 1, 11, 11, 5, 5, 5, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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]
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, 15, 19, 19, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 38, 19] 38
rigid atoms, others: [32, 33, 37, 38, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 39, 40])
total number of confs: 97
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040489 none CC1=CC=C(C(=O)NN=C2CCC(C(=O)[O-])C(C)C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 5, 1, 11, 11, 5, 5, 5, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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]
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: [1, 1, 1, 1, 1, 1, 8, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 2, 2, 2, 1, 1, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 1] 38
rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 42
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040489 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040489
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040489/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040489
Building REAL300000040490
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040490'
/scratch/stefan/7769621/working/building/REAL300000040490 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040490

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040490/0 /scratch/stefan/7769621/working/building/REAL300000040490 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 585)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/585
`/scratch/stefan/7769621/working/3D/585' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=C2CC(C(=O)[O-])(C3=CC=CC(Cl)=C3)C2)C(O)=C1)

`REAL300000040490.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040490.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040490/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040490 none CC1=CC=C(C(=O)NN=C2CC(C(=O)[O-])(C3=CC=CC(Cl)=C3)C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 5, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 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]
1  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [46, 41, 46, 46, 23, 23, 23, 10, 10, 10, 10, 1, 10, 14, 14, 1, 1, 1, 1, 1, 1, 1, 10, 46, 46, 46, 46, 46, 46, 46, 46, 23, 10, 10, 1, 1, 1, 1, 10, 10, 92, 46] 92
rigid atoms, others: [34, 35, 36, 37, 11, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 220
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040490 none CC1=CC=C(C(=O)NN=C2CC(C(=O)[O-])(C3=CC=CC(Cl)=C3)C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 5, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 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]
1  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [21, 14, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 1, 3, 3, 1, 10, 10, 4, 10, 10, 10, 1, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 10, 10, 9, 10, 1, 1, 42, 21] 92
rigid atoms, others: [32, 33, 38, 7, 8, 9, 10, 11, 12, 15, 22, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 40, 41])
total number of confs: 140
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040490 none CC1=CC=C(C(=O)NN=C2CC(C(=O)[O-])(C3=CC=CC(Cl)=C3)C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 5, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 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]
1  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 21, 21, 21, 21, 31, 31, 21, 46, 46, 37, 46, 46, 46, 21, 1, 1, 1, 2, 2, 2, 1, 1, 8, 21, 21, 46, 46, 46, 46, 21, 21, 2, 1] 92
rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 165
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040490 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040490
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040490/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040490
Building REAL300000040491
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040491'
/scratch/stefan/7769621/working/building/REAL300000040491 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040491

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040491/0 /scratch/stefan/7769621/working/building/REAL300000040491 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 586)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/586
`/scratch/stefan/7769621/working/3D/586' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=C2CCCC3=CC(C(=O)[O-])=CC=C32)C(O)=C1)

`REAL300000040491.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040491.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040491/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040491 none CC1=CC=C(C(=O)NN=C2CCCC3=CC(C(=O)[O-])=CC=C32)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 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]
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: [14, 14, 14, 14, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 14] 28
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 40, 41, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 55
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040491 none CC1=CC=C(C(=O)NN=C2CCCC3=CC(C(=O)[O-])=CC=C32)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 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]
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: [1, 1, 1, 1, 1, 1, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 2, 2, 2, 1, 1, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 1] 28
rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 22, 23, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 34
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040491 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040491
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040491/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040491
Building REAL300000040492
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040492'
/scratch/stefan/7769621/working/building/REAL300000040492 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040492

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040492/0 /scratch/stefan/7769621/working/building/REAL300000040492 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 587)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/587
`/scratch/stefan/7769621/working/3D/587' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1(C(=O)[O-])CCC1)=NNC(=O)C1=CC=C(C)C=C1O)

`REAL300000040492.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040492.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040492/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040492 none CC(CC1(C(=O)[O-])CCC1)=NNC(=O)C1=CC=C(C)C=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 1, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 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]
1  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: [12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 2, 2, 2, 1, 2] 36
rigid atoms, others: [34, 35, 39, 12, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 40])
total number of confs: 62
number of broken/clashed sets: 31
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040492 none CC(CC1(C(=O)[O-])CCC1)=NNC(=O)C1=CC=C(C)C=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 1, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 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]
1  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [10, 6, 1, 1, 1, 3, 3, 1, 1, 1, 10, 10, 14, 14, 14, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 14, 18, 18, 18, 18, 18, 18, 36] 36
rigid atoms, others: [32, 2, 3, 4, 7, 8, 9, 27, 28, 29, 30, 31] set([0, 1, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 101
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040492 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040492
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040492/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040492
Building REAL300000040493
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040493'
/scratch/stefan/7769621/working/building/REAL300000040493 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040493

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040493/0 /scratch/stefan/7769621/working/building/REAL300000040493 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 588)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/588
`/scratch/stefan/7769621/working/3D/588' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1)

`REAL300000040493.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040493.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040493/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040493 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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]
1  hydrogens need rotated
76  conformations in input
total number of sets (complete confs): 76
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 19, 19, 19, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 19, 38, 38, 38, 38, 38, 38, 76, 2, 2, 1, 1, 2, 2, 2, 1] 76
rigid atoms, others: [1, 41, 42, 46, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45])
total number of confs: 182
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040493 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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]
1  hydrogens need rotated
76  conformations in input
total number of sets (complete confs): 76
using faster count positions algorithm for large data
unique positions, atoms: [26, 26, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 26, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 26, 26, 26, 10, 1, 1, 2, 2, 2, 1, 2, 38, 38, 38, 38, 38, 38, 38, 38] 76
rigid atoms, others: [32, 33, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 74
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040493 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040493
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040493/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040493
Building REAL300000040494
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040494'
/scratch/stefan/7769621/working/building/REAL300000040494 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040494

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040494/0 /scratch/stefan/7769621/working/building/REAL300000040494 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 589)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/589
`/scratch/stefan/7769621/working/3D/589' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC(C(=O)[O-])=C(C)C=C2C)C(O)=C1)

`REAL300000040494.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040494.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040494/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040494 none CC1=CC=C(C(=O)NN=CC2=CC(C(=O)[O-])=C(C)C=C2C)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 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]
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, 67, 81, 81, 34, 34, 34, 13, 13, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 81, 81, 81, 34, 13, 1, 2, 2, 2, 1, 2, 2, 2, 162, 81] 162
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])
total number of confs: 401
number of broken/clashed sets: 24
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040494 none CC1=CC=C(C(=O)NN=CC2=CC(C(=O)[O-])=C(C)C=C2C)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 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]
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: [1, 1, 1, 1, 1, 1, 11, 11, 11, 25, 25, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 1, 1, 1, 2, 2, 2, 1, 1, 11, 25, 81, 81, 81, 81, 81, 81, 81, 81, 2, 1] 162
rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 21, 22, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 122
number of broken/clashed sets: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040494 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040494
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040494/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040494
Building REAL300000040495
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040495'
/scratch/stefan/7769621/working/building/REAL300000040495 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040495

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040495/0 /scratch/stefan/7769621/working/building/REAL300000040495 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 590)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/590
`/scratch/stefan/7769621/working/3D/590' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=CC(C(=O)[O-])=C2Cl)C(O)=C1)

`REAL300000040495.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040495.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040495/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040495 none CC1=CC=C(C(=O)NN=CC2=CC=CC(C(=O)[O-])=C2Cl)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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]
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: [21, 19, 21, 21, 11, 11, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 11, 6, 1, 1, 1, 42, 21] 42
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])
total number of confs: 100
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040495 none CC1=CC=C(C(=O)NN=CC2=CC=CC(C(=O)[O-])=C2Cl)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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]
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: [1, 1, 1, 1, 1, 1, 10, 10, 10, 17, 17, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 2, 2, 2, 1, 1, 10, 17, 21, 21, 21, 2, 1] 42
rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 45
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040495 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040495
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040495/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040495
Building REAL300000040496
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040496'
/scratch/stefan/7769621/working/building/REAL300000040496 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040496

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040496/0 /scratch/stefan/7769621/working/building/REAL300000040496 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 591)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/591
`/scratch/stefan/7769621/working/3D/591' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=C2CCCCC3=CC(C(=O)[O-])=CC=C32)C(O)=C1)

`REAL300000040496.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040496.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040496/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040496 none CC1=CC=C(C(=O)NN=C2CCCCC3=CC(C(=O)[O-])=CC=C32)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', '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', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 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]
1  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: [8, 6, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 8] 16
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 43, 44, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 36
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040496 none CC1=CC=C(C(=O)NN=C2CCCCC3=CC(C(=O)[O-])=CC=C32)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', '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', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 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]
1  hydrogens need rotated
16  conformations in input
total number of sets (complete confs): 16
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 2, 2, 2, 1, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 1] 16
rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 25
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040496 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040496
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040496/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040496
Building REAL300000040497
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040497'
/scratch/stefan/7769621/working/building/REAL300000040497 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040497

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040497/0 /scratch/stefan/7769621/working/building/REAL300000040497 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 592)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/592
`/scratch/stefan/7769621/working/3D/592' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=C(C(=O)[O-])C=NN2C)C(O)=C1)

`REAL300000040497.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040497.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040497/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040497 none CC1=CC=C(C(=O)NN=CC2=C(C(=O)[O-])C=NN2C)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 11, 11, 1, 8, 8, 5, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 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: [14, 11, 14, 14, 6, 6, 6, 4, 4, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 6, 4, 1, 2, 2, 2, 28, 14] 28
rigid atoms, others: [9, 10, 11, 12, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34])
total number of confs: 77
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040497 none CC1=CC=C(C(=O)NN=CC2=C(C(=O)[O-])C=NN2C)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 11, 11, 1, 8, 8, 5, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 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: [1, 1, 1, 1, 1, 1, 8, 8, 8, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 2, 2, 2, 1, 1, 8, 13, 14, 14, 14, 14, 2, 1] 28
rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 36
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040497 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040497
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040497/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040497
Building REAL300000040498
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040498'
/scratch/stefan/7769621/working/building/REAL300000040498 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040498

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040498/0 /scratch/stefan/7769621/working/building/REAL300000040498 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 593)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/593
`/scratch/stefan/7769621/working/3D/593' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=C(C(=O)[O-])C(F)=C2)C(O)=C1)

`REAL300000040498.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040498.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040498/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040498 none CC1=CC=C(C(=O)NN=CC2=CC=C(C(=O)[O-])C(F)=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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]
1  hydrogens need rotated
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [41, 40, 41, 41, 22, 22, 22, 10, 10, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 22, 10, 1, 1, 1, 82, 41] 82
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])
total number of confs: 179
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040498 none CC1=CC=C(C(=O)NN=CC2=CC=C(C(=O)[O-])C(F)=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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]
1  hydrogens need rotated
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 23, 23, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 2, 2, 2, 1, 1, 10, 23, 41, 41, 41, 2, 1] 82
rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 84
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040498 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040498
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040498/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040498
Building REAL300000040499
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040499'
/scratch/stefan/7769621/working/building/REAL300000040499 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040499

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040499/0 /scratch/stefan/7769621/working/building/REAL300000040499 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 594)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/594
`/scratch/stefan/7769621/working/3D/594' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=C(C=CC(=O)[O-])O2)C(O)=C1)

`REAL300000040499.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040499.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040499/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040499 none CC1=CC=C(C(=O)NN=CC2=CC=C(C=CC(=O)[O-])O2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [42, 26, 42, 42, 17, 17, 17, 4, 4, 1, 1, 1, 1, 1, 1, 10, 10, 21, 21, 1, 42, 42, 42, 42, 42, 42, 42, 42, 16, 4, 1, 1, 10, 10, 84, 42] 134
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])
total number of confs: 274
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040499 none CC1=CC=C(C(=O)NN=CC2=CC=C(C=CC(=O)[O-])O2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
134  conformations in input
total number of sets (complete confs): 134
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 11, 11, 29, 29, 42, 42, 42, 42, 67, 67, 67, 67, 42, 1, 1, 1, 2, 2, 2, 1, 1, 11, 29, 42, 42, 67, 67, 2, 1] 134
rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 162
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040499 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040499
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040499/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040499
Building REAL300000040500
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040500'
/scratch/stefan/7769621/working/building/REAL300000040500 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040500

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040500/0 /scratch/stefan/7769621/working/building/REAL300000040500 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 595)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/595
`/scratch/stefan/7769621/working/3D/595' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC(C(=O)[O-])=CC=C1OC(C)C)

`REAL300000040500.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040500.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040500/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040500 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 4, 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]
1  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 17, 17, 17, 39, 39, 27, 39, 39, 39, 39, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 16, 16, 6, 6, 6, 17, 39, 39, 39, 39, 39, 39, 78, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16] 102
rigid atoms, others: [1, 38, 39, 40, 14, 15, 16, 17, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 246
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040500 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 4, 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]
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: [20, 20, 11, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 20, 39, 39, 39, 39, 39, 39, 39, 39, 39, 51, 51, 51, 20, 20, 20, 11, 1, 1, 2, 2, 2, 1, 2, 39, 39, 39, 51, 51, 51, 51, 51, 51, 51] 102
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 11, 12, 13, 36, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 99
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040500 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040500
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040500/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040500
Building REAL300000040501
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040501'
/scratch/stefan/7769621/working/building/REAL300000040501 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040501

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040501/0 /scratch/stefan/7769621/working/building/REAL300000040501 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 596)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/596
`/scratch/stefan/7769621/working/3D/596' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=C2CCC3=CC=CC(C(=O)[O-])=C32)C(O)=C1)

`REAL300000040501.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040501.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040501/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040501 none CC1=CC=C(C(=O)NN=C2CCC3=CC=CC(C(=O)[O-])=C32)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [18, 18, 18, 18, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 18, 18, 18, 18, 18, 18, 18, 18, 8, 1, 1, 1, 1, 1, 1, 1, 36, 18] 36
rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 38, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37])
total number of confs: 71
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040501 none CC1=CC=C(C(=O)NN=C2CCC3=CC=CC(C(=O)[O-])=C32)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 2, 2, 2, 1, 1, 8, 18, 18, 18, 18, 18, 18, 18, 2, 1] 36
rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 21, 22, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 40
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040501 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040501
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040501/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040501
Building REAL300000040502
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040502'
/scratch/stefan/7769621/working/building/REAL300000040502 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040502

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040502/0 /scratch/stefan/7769621/working/building/REAL300000040502 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 597)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/597
`/scratch/stefan/7769621/working/3D/597' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)C(O)=C1)

`REAL300000040502.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040502.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040502/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040502 none CC1=CC=C(C(=O)NN=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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]
1  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: [22, 22, 22, 22, 12, 12, 12, 6, 6, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 12, 6, 3, 3, 1, 1, 1, 1, 3, 3, 44, 22] 44
rigid atoms, others: [37, 38, 39, 40, 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, 41, 42, 43, 44])
total number of confs: 106
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: REAL300000040502 none CC1=CC=C(C(=O)NN=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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]
1  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: [22, 20, 22, 22, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 3, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 11, 5, 1, 1, 3, 3, 3, 3, 1, 1, 44, 22] 44
rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 43, 44])
total number of confs: 114
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040502 none CC1=CC=C(C(=O)NN=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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]
1  hydrogens need rotated
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 16, 16, 22, 22, 16, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 2, 2, 2, 1, 1, 8, 16, 22, 22, 22, 22, 22, 22, 22, 22, 2, 1] 44
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 44, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 77
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040502 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040502
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040502/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040502
Building REAL300000040503
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040503'
/scratch/stefan/7769621/working/building/REAL300000040503 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040503

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040503/0 /scratch/stefan/7769621/working/building/REAL300000040503 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 598)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/598
`/scratch/stefan/7769621/working/3D/598' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CN=CC(C(=O)[O-])=C1)

`REAL300000040503.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040503.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040503/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040503 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 16, 16, 16, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 2, 2, 1, 9, 9, 9, 16, 30, 30, 30, 30, 30, 30, 60, 1, 1, 1] 60
rigid atoms, others: [1, 34, 35, 36, 14, 15, 16, 17, 18, 19, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 128
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040503 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 20, 30, 30, 30, 30, 30, 30, 30, 30, 20, 20, 20, 9, 1, 1, 2, 2, 2, 1, 2, 30, 30, 30] 60
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 61
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040503 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040503
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040503/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040503
Building REAL300000040504
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040504'
/scratch/stefan/7769621/working/building/REAL300000040504 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040504

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040504/0 /scratch/stefan/7769621/working/building/REAL300000040504 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 599)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/599
`/scratch/stefan/7769621/working/3D/599' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CNC3=CC=C(C(=O)[O-])C=C23)C(O)=C1)

`REAL300000040504.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040504.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040504/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040504 none CC1=CC=C(C(=O)NN=CC2=CNC3=CC=C(C(=O)[O-])C=C23)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 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]
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, 19, 19, 19, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 8, 4, 1, 1, 1, 1, 1, 38, 19] 38
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])
total number of confs: 77
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040504 none CC1=CC=C(C(=O)NN=CC2=CNC3=CC=C(C(=O)[O-])C=C23)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 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]
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: [1, 1, 1, 1, 1, 1, 10, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 2, 2, 2, 1, 1, 10, 19, 19, 19, 19, 19, 19, 2, 1] 38
rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 22, 23, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 43
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040504 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040504
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040504/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040504
Building REAL300000040505
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040505'
/scratch/stefan/7769621/working/building/REAL300000040505 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040505

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040505/0 /scratch/stefan/7769621/working/building/REAL300000040505 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 600)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/600
`/scratch/stefan/7769621/working/3D/600' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=C(C(=O)[O-])C(O)=C2)C(O)=C1)

`REAL300000040505.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040505.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040505/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040505 none CC1=CC=C(C(=O)NN=CC2=CC=C(C(=O)[O-])C(O)=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [37, 37, 37, 37, 24, 25, 25, 9, 9, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 25, 9, 1, 1, 2, 1, 74, 37] 148
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])
total number of confs: 166
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040505 none CC1=CC=C(C(=O)NN=CC2=CC=C(C(=O)[O-])C(O)=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 20, 20, 37, 37, 37, 37, 37, 37, 37, 37, 36, 1, 1, 1, 2, 2, 2, 1, 1, 10, 20, 37, 37, 74, 37, 2, 1] 148
rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 153
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040505 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040505
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040505/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040505
Building REAL300000040506
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040506'
/scratch/stefan/7769621/working/building/REAL300000040506 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040506

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040506/0 /scratch/stefan/7769621/working/building/REAL300000040506 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 601)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/601
`/scratch/stefan/7769621/working/3D/601' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=C(C)C(C(=O)[O-])=C2)C(O)=C1)

`REAL300000040506.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040506.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040506/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040506 none CC1=CC=C(C(=O)NN=CC2=CC=C(C)C(C(=O)[O-])=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [20, 20, 20, 20, 11, 12, 12, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 20, 20, 20, 20, 20, 20, 20, 20, 12, 9, 1, 1, 2, 2, 2, 1, 40, 20] 40
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])
total number of confs: 94
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040506 none CC1=CC=C(C(=O)NN=CC2=CC=C(C)C(C(=O)[O-])=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 14, 14, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 2, 2, 2, 1, 1, 8, 14, 20, 20, 20, 20, 20, 20, 2, 1] 40
rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 22, 26, 27, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 42
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040506 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040506
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040506/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040506
Building REAL300000040507
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040507'
/scratch/stefan/7769621/working/building/REAL300000040507 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040507

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040507/0 /scratch/stefan/7769621/working/building/REAL300000040507 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 602)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/602
`/scratch/stefan/7769621/working/3D/602' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC(C(=O)[O-])=C(Cl)S2)C(O)=C1)

`REAL300000040507.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040507.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040507/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040507 none CC1=CC=C(C(=O)NN=CC2=CC(C(=O)[O-])=C(Cl)S2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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]
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, 53, 63, 63, 27, 27, 27, 11, 11, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 63, 63, 63, 63, 63, 63, 63, 63, 27, 11, 1, 126, 63] 126
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])
total number of confs: 292
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040507 none CC1=CC=C(C(=O)NN=CC2=CC(C(=O)[O-])=C(Cl)S2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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]
1  hydrogens need rotated
126  conformations in input
total number of sets (complete confs): 126
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 26, 26, 63, 63, 63, 63, 63, 63, 63, 63, 1, 1, 1, 2, 2, 2, 1, 1, 10, 26, 63, 2, 1] 126
rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 25, 26, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30])
total number of confs: 108
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040507 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040507
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040507/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040507
Building REAL300000040508
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040508'
/scratch/stefan/7769621/working/building/REAL300000040508 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040508

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040508/0 /scratch/stefan/7769621/working/building/REAL300000040508 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 603)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/603
`/scratch/stefan/7769621/working/3D/603' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=C(C(=O)[O-])C=C1C)

`REAL300000040508.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040508.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040508/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040508 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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.3', '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, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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]
1  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 8, 19, 19, 19, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 8, 8, 8, 19, 33, 33, 33, 33, 33, 33, 66, 1, 1, 1, 2, 2, 2] 66
rigid atoms, others: [1, 35, 36, 37, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40])
total number of confs: 145
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040508 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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.3', '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, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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]
1  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 18, 33, 33, 28, 33, 33, 33, 33, 33, 33, 19, 19, 19, 10, 1, 1, 2, 2, 2, 1, 2, 33, 33, 33, 33, 33, 33] 66
rigid atoms, others: [33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 95
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040508 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040508
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040508/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040508
Building REAL300000040509
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040509'
/scratch/stefan/7769621/working/building/REAL300000040509 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040509

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040509/0 /scratch/stefan/7769621/working/building/REAL300000040509 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 604)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/604
`/scratch/stefan/7769621/working/3D/604' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC(Cl)=NC=C2C(=O)[O-])C(O)=C1)

`REAL300000040509.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040509.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040509/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040509 none CC1=CC=C(C(=O)NN=CC2=CC(Cl)=NC=C2C(=O)[O-])C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 16, 8, 1, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 21, 21, 21, 10, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 10, 6, 1, 1, 42, 21] 42
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33])
total number of confs: 90
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040509 none CC1=CC=C(C(=O)NN=CC2=CC(Cl)=NC=C2C(=O)[O-])C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 16, 8, 1, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 7, 7, 7, 10, 10, 21, 21, 21, 10, 21, 21, 21, 21, 21, 1, 1, 1, 2, 2, 2, 1, 1, 7, 10, 21, 21, 2, 1] 42
rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32])
total number of confs: 71
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040509 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040509
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040509/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040509
Building REAL300000040510
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040510'
/scratch/stefan/7769621/working/building/REAL300000040510 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040510

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040510/0 /scratch/stefan/7769621/working/building/REAL300000040510 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 605)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/605
`/scratch/stefan/7769621/working/3D/605' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC(C(=O)[O-])=NN2C)C(O)=C1)

`REAL300000040510.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040510.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040510/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040510 none CC1=CC=C(C(=O)NN=CC2=CC(C(=O)[O-])=NN2C)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 8, 5, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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]
1  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [23, 23, 23, 23, 16, 16, 16, 7, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 16, 7, 1, 2, 2, 2, 46, 23] 46
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: 108
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040510 none CC1=CC=C(C(=O)NN=CC2=CC(C(=O)[O-])=NN2C)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 8, 8, 5, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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]
1  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 17, 17, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 2, 2, 2, 1, 1, 8, 17, 23, 23, 23, 23, 2, 1] 46
rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 47
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040510 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040510
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040510/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040510
Building REAL300000040511
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040511'
/scratch/stefan/7769621/working/building/REAL300000040511 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040511

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040511/0 /scratch/stefan/7769621/working/building/REAL300000040511 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 606)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/606
`/scratch/stefan/7769621/working/3D/606' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)C(O)=C1)

`REAL300000040511.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040511.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040511/0/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', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040511 none CC1=CC=C(C(=O)NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 4, 7, 7, 7, 7, 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, 44, 44, 44, 26, 26, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 67, 67, 67, 67, 67, 67, 67, 67, 44, 26, 12, 12, 1, 1, 2, 1, 134, 67] 268
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])
total number of confs: 294
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: REAL300000040511 none CC1=CC=C(C(=O)NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 4, 7, 7, 7, 7, 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: [34, 25, 34, 34, 16, 16, 16, 5, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 13, 13, 12, 1, 34, 34, 34, 34, 34, 34, 34, 34, 16, 5, 1, 1, 12, 12, 24, 12, 68, 34] 268
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])
total number of confs: 214
number of broken/clashed sets: 54
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040511 none CC1=CC=C(C(=O)NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 4, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 9, 9, 9, 25, 25, 34, 34, 34, 34, 67, 67, 67, 67, 67, 67, 67, 67, 67, 34, 1, 1, 1, 2, 2, 2, 1, 1, 9, 25, 34, 34, 67, 67, 134, 67, 2, 1] 268
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 42, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 245
number of broken/clashed sets: 54
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040511 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040511
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040511/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040511
Building REAL300000040512
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040512'
/scratch/stefan/7769621/working/building/REAL300000040512 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040512

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040512/0 /scratch/stefan/7769621/working/building/REAL300000040512 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 607)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/607
`/scratch/stefan/7769621/working/3D/607' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC(C(=O)[O-])=CN2C)C(O)=C1)

`REAL300000040512.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040512.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040512/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040512 none CC1=CC=C(C(=O)NN=CC2=CC(C(=O)[O-])=CN2C)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.pl3', 'C.3', '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, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 8, 5, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 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]
1  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: [20, 19, 20, 20, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 12, 6, 1, 1, 2, 2, 2, 40, 20] 40
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])
total number of confs: 94
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040512 none CC1=CC=C(C(=O)NN=CC2=CC(C(=O)[O-])=CN2C)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.pl3', 'C.3', '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, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 8, 5, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 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]
1  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 15, 15, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 2, 2, 2, 1, 1, 8, 15, 20, 20, 20, 20, 20, 2, 1] 40
rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 43
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040512 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040512
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040512/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040512
Building REAL300000040513
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040513'
/scratch/stefan/7769621/working/building/REAL300000040513 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040513

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040513/0 /scratch/stefan/7769621/working/building/REAL300000040513 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 608)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/608
`/scratch/stefan/7769621/working/3D/608' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC(C(=O)[O-])=CC=C2N(C)C)C(O)=C1)

`REAL300000040513.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040513.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040513/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040513 none CC1=CC=C(C(=O)NN=CC2=CC(C(=O)[O-])=CC=C2N(C)C)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.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, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 5, 5, 1, 12, 1, 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, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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]
1  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: [9, 9, 9, 9, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 5, 4, 1, 1, 1, 2, 2, 2, 1, 1, 1, 18, 9] 18
rigid atoms, others: [32, 33, 34, 38, 39, 40, 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, 35, 36, 37, 41, 42])
total number of confs: 43
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040513 none CC1=CC=C(C(=O)NN=CC2=CC(C(=O)[O-])=CC=C2N(C)C)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.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, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 5, 5, 1, 12, 1, 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, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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]
1  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 2, 2, 2, 1, 1, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 1] 18
rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 22, 23, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 26
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040513 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040513
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040513/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040513
Building REAL300000040514
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040514'
/scratch/stefan/7769621/working/building/REAL300000040514 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040514

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040514/0 /scratch/stefan/7769621/working/building/REAL300000040514 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 609)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/609
`/scratch/stefan/7769621/working/3D/609' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])C=C(C=NNC(=O)C2=CC=C(C)C=C2O)O1)

`REAL300000040514.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040514.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040514/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040514 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)C2=CC=C(C)C=C2O)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 3, 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, 60, 32, 32, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 60, 33, 11, 1, 1, 2, 2, 2, 1, 2] 120
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 34])
total number of confs: 112
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040514 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)C2=CC=C(C)C=C2O)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 3, 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: [1, 1, 1, 1, 3, 3, 1, 1, 1, 9, 9, 24, 24, 24, 60, 60, 50, 60, 60, 60, 60, 1, 2, 2, 2, 1, 9, 24, 60, 60, 60, 60, 60, 60, 119] 120
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 21, 25] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 278
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040514 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040514
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040514/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040514
Building REAL300000040515
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040515'
/scratch/stefan/7769621/working/building/REAL300000040515 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040515

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040515/0 /scratch/stefan/7769621/working/building/REAL300000040515 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 610)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/610
`/scratch/stefan/7769621/working/3D/610' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)S2)C(O)=C1)

`REAL300000040515.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040515.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040515/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040515 none CC1=CC=C(C(=O)NN=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)S2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 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]
1  hydrogens need rotated
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [70, 70, 70, 70, 47, 47, 47, 25, 25, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 70, 70, 70, 70, 70, 70, 70, 70, 47, 25, 7, 7, 1, 1, 1, 1, 140, 70] 140
rigid atoms, others: [36, 37, 38, 39, 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, 40, 41])
total number of confs: 308
number of broken/clashed sets: 25
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040515 none CC1=CC=C(C(=O)NN=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)S2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 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]
1  hydrogens need rotated
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [37, 37, 37, 37, 23, 23, 23, 9, 9, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 7, 7, 7, 7, 1, 37, 37, 37, 37, 37, 37, 37, 37, 23, 9, 1, 1, 7, 7, 7, 7, 74, 37] 140
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])
total number of confs: 186
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040515 none CC1=CC=C(C(=O)NN=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)S2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 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]
1  hydrogens need rotated
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 26, 26, 37, 37, 37, 37, 70, 70, 37, 39, 70, 70, 70, 70, 37, 1, 1, 1, 2, 2, 2, 1, 1, 9, 26, 37, 37, 70, 70, 70, 70, 2, 1] 140
rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 332
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040515 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040515
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040515/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040515
Building REAL300000040516
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040516'
/scratch/stefan/7769621/working/building/REAL300000040516 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040516

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040516/0 /scratch/stefan/7769621/working/building/REAL300000040516 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 611)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/611
`/scratch/stefan/7769621/working/3D/611' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)C(O)=C1)

`REAL300000040516.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040516.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040516/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040516 none CC1=CC=C(C(=O)NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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]
1  hydrogens need rotated
324  conformations in input
total number of sets (complete confs): 324
using faster count positions algorithm for large data
unique positions, atoms: [162, 162, 162, 162, 113, 113, 113, 51, 51, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 162, 162, 162, 162, 162, 162, 162, 162, 113, 51, 12, 12, 1, 1, 1, 1, 324, 162] 324
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])
total number of confs: 703
number of broken/clashed sets: 60
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040516 none CC1=CC=C(C(=O)NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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]
1  hydrogens need rotated
324  conformations in input
total number of sets (complete confs): 324
using faster count positions algorithm for large data
unique positions, atoms: [75, 54, 75, 75, 31, 30, 31, 9, 9, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 13, 13, 12, 1, 75, 75, 75, 75, 75, 75, 75, 75, 30, 9, 1, 1, 12, 12, 12, 12, 150, 75] 324
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])
total number of confs: 386
number of broken/clashed sets: 60
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040516 none CC1=CC=C(C(=O)NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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]
1  hydrogens need rotated
324  conformations in input
total number of sets (complete confs): 324
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 36, 36, 75, 75, 75, 75, 162, 162, 162, 162, 162, 162, 162, 162, 75, 1, 1, 1, 2, 2, 2, 1, 1, 10, 36, 75, 75, 162, 162, 162, 162, 2, 1] 324
rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 248
number of broken/clashed sets: 60
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040516 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040516
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040516/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040516
Building REAL300000040517
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040517'
/scratch/stefan/7769621/working/building/REAL300000040517 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040517

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040517/0 /scratch/stefan/7769621/working/building/REAL300000040517 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 612)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/612
`/scratch/stefan/7769621/working/3D/612' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC(C(=O)[O-])=C(C=NNC(=O)C2=CC=C(C)C=C2O)S1)

`REAL300000040517.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040517.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040517/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040517 none CCC1=CC(C(=O)[O-])=C(C=NNC(=O)C2=CC=C(C)C=C2O)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [46, 26, 26, 26, 24, 26, 27, 27, 21, 21, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 26, 46, 46, 46, 46, 46, 26, 21, 10, 1, 1, 2, 2, 2, 1, 2] 92
rigid atoms, others: [32, 36, 12, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 37])
total number of confs: 184
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040517 none CCC1=CC(C(=O)[O-])=C(C=NNC(=O)C2=CC=C(C)C=C2O)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 1, 1, 1, 1, 3, 3, 1, 1, 4, 4, 11, 11, 11, 26, 26, 21, 26, 26, 26, 26, 1, 9, 9, 9, 8, 8, 1, 4, 11, 26, 26, 26, 26, 26, 26, 52] 92
rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 22, 28] set([0, 6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 160
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040517 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040517
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040517/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040517
Building REAL300000040518
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040518'
/scratch/stefan/7769621/working/building/REAL300000040518 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040518

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040518/0 /scratch/stefan/7769621/working/building/REAL300000040518 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 613)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/613
`/scratch/stefan/7769621/working/3D/613' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=C(C)C=C1O)

`REAL300000040518.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040518.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040518/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040518 none COC1=CC=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=C(C)C=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
190  conformations in input
total number of sets (complete confs): 190
using faster count positions algorithm for large data
unique positions, atoms: [95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 35, 35, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 95, 95, 95, 35, 10, 1, 1, 2, 2, 2, 1, 2] 190
rigid atoms, others: [32, 33, 37, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 38])
total number of confs: 142
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040518 none COC1=CC=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=C(C)C=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
190  conformations in input
total number of sets (complete confs): 190
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 12, 12, 38, 38, 38, 95, 95, 83, 95, 95, 95, 95, 4, 4, 4, 1, 1, 1, 12, 38, 95, 95, 95, 95, 95, 95, 190] 190
rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 27, 28, 29] set([0, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 437
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040518 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040518
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040518/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040518
Building REAL300000040519
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040519'
/scratch/stefan/7769621/working/building/REAL300000040519 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040519

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040519/0 /scratch/stefan/7769621/working/building/REAL300000040519 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 614)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/614
`/scratch/stefan/7769621/working/3D/614' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)C(O)=C1)

`REAL300000040519.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040519.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040519/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040519 none CC1=CC=C(C(=O)NN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 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]
1  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [18, 18, 18, 18, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 7, 4, 1, 1, 1, 1, 36, 18] 36
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, 36, 37, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 71
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040519 none CC1=CC=C(C(=O)NN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 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]
1  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 2, 2, 2, 1, 1, 10, 18, 18, 18, 18, 18, 2, 1] 36
rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 23, 24, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 42
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040519 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040519
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040519/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040519
Building REAL300000040520
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040520'
/scratch/stefan/7769621/working/building/REAL300000040520 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040520

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040520/0 /scratch/stefan/7769621/working/building/REAL300000040520 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 615)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/615
`/scratch/stefan/7769621/working/3D/615' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=C2CCCC3=NC=C(C(=O)[O-])C=C23)C(O)=C1)

`REAL300000040520.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040520.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040520/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040520 none CC1=CC=C(C(=O)NN=C2CCCC3=NC=C(C(=O)[O-])C=C23)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 5, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 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]
1  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 10, 1, 1, 1, 1, 1, 1, 1, 1, 30, 15] 30
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 39, 40, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 64
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040520 none CC1=CC=C(C(=O)NN=C2CCCC3=NC=C(C(=O)[O-])C=C23)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 5, 5, 5, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 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]
1  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 2, 2, 2, 1, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 2, 1] 30
rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 22, 23, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 33
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040520 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040520
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040520/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040520
Building REAL300000040521
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040521'
/scratch/stefan/7769621/working/building/REAL300000040521 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040521

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040521/0 /scratch/stefan/7769621/working/building/REAL300000040521 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 616)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/616
`/scratch/stefan/7769621/working/3D/616' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC(C(=O)[O-])=CC=C2Br)C(O)=C1)

`REAL300000040521.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040521.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040521/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040521 none CC1=CC=C(C(=O)NN=CC2=CC(C(=O)[O-])=CC=C2Br)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [52, 52, 52, 52, 30, 30, 30, 12, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 52, 52, 52, 52, 52, 52, 52, 52, 30, 12, 1, 1, 1, 104, 52] 104
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])
total number of confs: 220
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040521 none CC1=CC=C(C(=O)NN=CC2=CC(C(=O)[O-])=CC=C2Br)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
104  conformations in input
total number of sets (complete confs): 104
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 25, 25, 52, 52, 52, 52, 52, 52, 52, 51, 52, 1, 1, 1, 2, 2, 2, 1, 1, 10, 25, 52, 52, 52, 2, 1] 104
rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 96
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040521 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040521
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040521/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040521
Building REAL300000040522
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040522'
/scratch/stefan/7769621/working/building/REAL300000040522 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040522

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040522/0 /scratch/stefan/7769621/working/building/REAL300000040522 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 617)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/617
`/scratch/stefan/7769621/working/3D/617' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=C(C)C=C2C(=O)[O-])C(O)=C1)

`REAL300000040522.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040522.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040522/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040522 none CC1=CC=C(C(=O)NN=CC2=CC=C(C)C=C2C(=O)[O-])C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [20, 19, 20, 20, 9, 9, 9, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 9, 6, 1, 1, 2, 2, 2, 1, 40, 20] 40
rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 36, 37])
total number of confs: 95
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040522 none CC1=CC=C(C(=O)NN=CC2=CC=C(C)C=C2C(=O)[O-])C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 2, 2, 2, 1, 1, 7, 10, 20, 20, 20, 20, 20, 20, 2, 1] 40
rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 22, 26, 27, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 44
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040522 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040522
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040522/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040522
Building REAL300000040523
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040523'
/scratch/stefan/7769621/working/building/REAL300000040523 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040523

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040523/0 /scratch/stefan/7769621/working/building/REAL300000040523 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 618)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/618
`/scratch/stefan/7769621/working/3D/618' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)C2=CC=C(C)C=C2O)=CC=C1C(=O)[O-])

`REAL300000040523.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040523.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040523/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040523 none COC1=CC(C=NNC(=O)C2=CC=C(C)C=C2O)=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 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]
1  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: [83, 74, 74, 73, 31, 31, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 83, 83, 83, 83, 83, 74, 31, 10, 1, 1, 2, 2, 2, 1, 2, 74, 74] 166
rigid atoms, others: [35, 8, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 36, 37, 38])
total number of confs: 177
number of broken/clashed sets: 28
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040523 none COC1=CC(C=NNC(=O)C2=CC=C(C)C=C2O)=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 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]
1  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: [3, 1, 1, 1, 1, 1, 12, 12, 38, 38, 38, 74, 74, 62, 74, 74, 74, 74, 1, 1, 1, 1, 3, 3, 4, 4, 4, 1, 12, 38, 74, 74, 74, 74, 74, 74, 148, 1, 1] 166
rigid atoms, others: [1, 2, 3, 4, 5, 38, 18, 19, 20, 21, 27, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 354
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040523 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040523
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040523/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040523
Building REAL300000040524
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040524'
/scratch/stefan/7769621/working/building/REAL300000040524 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040524

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040524/0 /scratch/stefan/7769621/working/building/REAL300000040524 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 619)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/619
`/scratch/stefan/7769621/working/3D/619' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=C(F)C=C(C(=O)[O-])C=C2F)C(O)=C1)

`REAL300000040524.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040524.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040524/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040524 none CC1=CC=C(C(=O)NN=CC2=C(F)C=C(C(=O)[O-])C=C2F)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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]
1  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: [25, 25, 25, 25, 13, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 13, 7, 1, 1, 50, 25] 50
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])
total number of confs: 109
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040524 none CC1=CC=C(C(=O)NN=CC2=C(F)C=C(C(=O)[O-])C=C2F)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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]
1  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 20, 20, 25, 25, 25, 20, 20, 25, 25, 25, 25, 25, 1, 1, 1, 2, 2, 2, 1, 1, 8, 20, 25, 25, 2, 1] 50
rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 21, 22, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33])
total number of confs: 87
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040524 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040524
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040524/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040524
Building REAL300000040525
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040525'
/scratch/stefan/7769621/working/building/REAL300000040525 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040525

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040525/0 /scratch/stefan/7769621/working/building/REAL300000040525 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 620)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/620
`/scratch/stefan/7769621/working/3D/620' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])NC(C=NNC(=O)C2=CC=C(C)C=C2O)=C1)

`REAL300000040525.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040525.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040525/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040525 none CC1=C(C(=O)[O-])NC(C=NNC(=O)C2=CC=C(C)C=C2O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [59, 59, 59, 59, 59, 59, 59, 32, 32, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 32, 10, 1, 1, 2, 2, 2, 1, 2, 59] 118
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 34, 35])
total number of confs: 103
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040525 none CC1=C(C(=O)[O-])NC(C=NNC(=O)C2=CC=C(C)C=C2O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 9, 9, 21, 21, 21, 59, 59, 44, 59, 59, 59, 59, 1, 2, 2, 2, 1, 9, 21, 58, 59, 59, 59, 59, 59, 118, 1] 118
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 35, 21, 25] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 278
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040525 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040525
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040525/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040525
Building REAL300000040526
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040526'
/scratch/stefan/7769621/working/building/REAL300000040526 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040526

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040526/0 /scratch/stefan/7769621/working/building/REAL300000040526 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 621)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/621
`/scratch/stefan/7769621/working/3D/621' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC(C(=O)[O-])=CC(Br)=C2O)C(O)=C1)

`REAL300000040526.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040526.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040526/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040526 none CC1=CC=C(C(=O)NN=CC2=CC(C(=O)[O-])=CC(Br)=C2O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [43, 43, 43, 43, 22, 22, 22, 12, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 22, 12, 1, 1, 2, 86, 43] 172
rigid atoms, others: [32, 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, 33, 34, 35])
total number of confs: 181
number of broken/clashed sets: 43
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040526 none CC1=CC=C(C(=O)NN=CC2=CC(C(=O)[O-])=CC(Br)=C2O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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, 1, 10, 10, 10, 26, 26, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 2, 2, 2, 1, 1, 10, 26, 43, 43, 86, 2, 1] 172
rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 21, 22, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34])
total number of confs: 165
number of broken/clashed sets: 43
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040526 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040526/1 /scratch/stefan/7769621/working/building/REAL300000040526 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 622)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/622
`/scratch/stefan/7769621/working/3D/622' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC(C(=O)[O-])=CC(Br)=C2[O-])C(O)=C1)

`REAL300000040526.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040526.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040526/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040526 none CC1=CC=C(C(=O)NN=CC2=CC(C(=O)[O-])=CC(Br)=C2[O-])C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [16, 16, 16, 16, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 9, 5, 1, 1, 32, 16] 32
rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 67
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040526 none CC1=CC=C(C(=O)NN=CC2=CC(C(=O)[O-])=CC(Br)=C2[O-])C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 2, 2, 2, 1, 1, 9, 16, 16, 16, 2, 1] 32
rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 21, 22, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33])
total number of confs: 38
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040526 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040526
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040526/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040526/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040526
Building REAL300000040527
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040527'
/scratch/stefan/7769621/working/building/REAL300000040527 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040527

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040527/0 /scratch/stefan/7769621/working/building/REAL300000040527 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 623)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/623
`/scratch/stefan/7769621/working/3D/623' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)C(O)=C1)

`REAL300000040527.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040527.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040527/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040527 none CC1=CC=C(C(=O)NN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 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]
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, 198, 201, 201, 134, 134, 134, 92, 92, 52, 51, 52, 52, 29, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 201, 201, 201, 201, 201, 201, 201, 201, 134, 92, 52, 52, 9, 9, 1, 1, 52, 52, 402, 201] 402
rigid atoms, others: [40, 41, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45])
total number of confs: 914
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: REAL300000040527 none CC1=CC=C(C(=O)NN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 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]
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: [55, 37, 55, 55, 20, 19, 20, 6, 6, 1, 1, 1, 1, 1, 1, 2, 12, 52, 52, 52, 52, 52, 52, 52, 1, 1, 55, 55, 55, 55, 55, 55, 55, 55, 19, 6, 1, 1, 12, 12, 52, 52, 1, 1, 110, 55] 402
rigid atoms, others: [43, 36, 37, 9, 10, 11, 12, 13, 14, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 44, 45])
total number of confs: 360
number of broken/clashed sets: 201
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040527 none CC1=CC=C(C(=O)NN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 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]
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, 11, 11, 11, 30, 30, 55, 55, 31, 55, 89, 144, 201, 201, 201, 201, 201, 201, 201, 55, 55, 1, 1, 1, 2, 2, 2, 1, 1, 11, 30, 55, 55, 144, 144, 201, 201, 54, 55, 2, 1] 402
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 45, 26, 27, 28, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 594
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040527 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040527
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040527/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040527
Building REAL300000040528
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040528'
/scratch/stefan/7769621/working/building/REAL300000040528 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040528

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040528/0 /scratch/stefan/7769621/working/building/REAL300000040528 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 624)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/624
`/scratch/stefan/7769621/working/3D/624' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)C(O)=C1)

`REAL300000040528.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040528.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040528/0/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040528 none CC1=CC=C(C(=O)NN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [26, 26, 26, 26, 18, 18, 18, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 18, 10, 2, 1, 1, 1, 1, 1, 52, 26] 104
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])
total number of confs: 116
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040528 none CC1=CC=C(C(=O)NN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
104  conformations in input
total number of sets (complete confs): 104
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 20, 20, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 2, 2, 2, 1, 1, 10, 20, 52, 26, 26, 26, 26, 26, 2, 1] 104
rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 105
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040528 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040528
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040528/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040528
Building REAL300000040529
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040529'
/scratch/stefan/7769621/working/building/REAL300000040529 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040529

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040529/0 /scratch/stefan/7769621/working/building/REAL300000040529 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 625)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/625
`/scratch/stefan/7769621/working/3D/625' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)C(O)=C1)

`REAL300000040529.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040529.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040529/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040529 none CC1=CC=C(C(=O)NN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
1  hydrogens need rotated
230  conformations in input
total number of sets (complete confs): 230
using faster count positions algorithm for large data
unique positions, atoms: [65, 63, 65, 65, 36, 36, 36, 16, 16, 3, 2, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 5, 5, 65, 65, 65, 65, 65, 65, 65, 65, 36, 16, 5, 5, 1, 1, 1, 2, 2, 1, 5, 5, 130, 65] 230
rigid atoms, others: [38, 39, 40, 43, 13, 14, 15, 16, 17, 18, 19, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 44, 45, 46, 47])
total number of confs: 310
number of broken/clashed sets: 40
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040529 none CC1=CC=C(C(=O)NN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
1  hydrogens need rotated
230  conformations in input
total number of sets (complete confs): 230
using faster count positions algorithm for large data
unique positions, atoms: [32, 24, 32, 32, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 19, 19, 5, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 15, 6, 1, 1, 5, 5, 5, 9, 9, 5, 1, 1, 64, 32] 230
rigid atoms, others: [45, 36, 37, 9, 10, 11, 12, 13, 14, 44, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 46, 47])
total number of confs: 216
number of broken/clashed sets: 40
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040529 none CC1=CC=C(C(=O)NN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
1  hydrogens need rotated
230  conformations in input
total number of sets (complete confs): 230
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 26, 26, 32, 32, 29, 26, 65, 65, 65, 65, 65, 115, 115, 115, 65, 32, 32, 1, 1, 1, 2, 2, 2, 1, 1, 10, 26, 32, 32, 65, 65, 65, 115, 115, 65, 32, 32, 2, 1] 230
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 47, 26, 27, 28, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 430
number of broken/clashed sets: 40
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040529 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040529
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040529/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040529
Building REAL300000040530
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040530'
/scratch/stefan/7769621/working/building/REAL300000040530 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040530

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040530/0 /scratch/stefan/7769621/working/building/REAL300000040530 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 626)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/626
`/scratch/stefan/7769621/working/3D/626' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=C(C(=O)[O-])C=C(Cl)S2)C(O)=C1)

`REAL300000040530.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040530.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040530/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040530 none CC1=CC=C(C(=O)NN=CC2=C(C(=O)[O-])C=C(Cl)S2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 16, 14, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 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: [21, 18, 21, 21, 10, 10, 10, 6, 6, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 9, 5, 1, 42, 21] 42
rigid atoms, others: [9, 10, 11, 12, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31])
total number of confs: 105
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040530 none CC1=CC=C(C(=O)NN=CC2=C(C(=O)[O-])C=C(Cl)S2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 16, 14, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 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: [1, 1, 1, 1, 1, 1, 9, 9, 9, 16, 16, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 2, 2, 2, 1, 1, 9, 16, 21, 2, 1] 42
rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 25, 26, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30])
total number of confs: 47
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040530 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040530
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040530/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040530
Building REAL300000040531
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040531'
/scratch/stefan/7769621/working/building/REAL300000040531 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040531

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040531/0 /scratch/stefan/7769621/working/building/REAL300000040531 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 627)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/627
`/scratch/stefan/7769621/working/3D/627' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=C(C(=O)[O-])C=CS2)C(O)=C1)

`REAL300000040531.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040531.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040531/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040531 none CC1=CC=C(C(=O)NN=CC2=C(C(=O)[O-])C=CS2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [22, 18, 22, 22, 9, 9, 10, 5, 5, 1, 1, 1, 1, 3, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 9, 5, 1, 1, 44, 22] 44
rigid atoms, others: [9, 10, 11, 12, 15, 16, 17, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 112
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040531 none CC1=CC=C(C(=O)NN=CC2=C(C(=O)[O-])C=CS2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 15, 15, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 2, 2, 2, 1, 1, 9, 15, 22, 22, 2, 1] 44
rigid atoms, others: [0, 1, 2, 3, 4, 5, 18, 19, 20, 24, 25, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30])
total number of confs: 49
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040531 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040531
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040531/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040531
Building REAL300000040532
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040532'
/scratch/stefan/7769621/working/building/REAL300000040532 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040532

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040532/0 /scratch/stefan/7769621/working/building/REAL300000040532 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 628)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/628
`/scratch/stefan/7769621/working/3D/628' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CSC(C(=O)[O-])=C2)C(O)=C1)

`REAL300000040532.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040532.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040532/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040532 none CC1=CC=C(C(=O)NN=CC2=CSC(C(=O)[O-])=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 14, 1, 1, 11, 11, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [28, 26, 28, 28, 18, 18, 18, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 28, 28, 28, 28, 28, 28, 28, 28, 18, 8, 1, 1, 56, 28] 56
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])
total number of confs: 126
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040532 none CC1=CC=C(C(=O)NN=CC2=CSC(C(=O)[O-])=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 14, 1, 1, 11, 11, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 20, 20, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 2, 2, 2, 1, 1, 9, 20, 28, 28, 2, 1] 56
rigid atoms, others: [0, 1, 2, 3, 4, 5, 18, 19, 20, 24, 25, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30])
total number of confs: 54
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040532 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040532
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040532/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040532
Building REAL300000040533
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040533'
/scratch/stefan/7769621/working/building/REAL300000040533 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040533

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040533/0 /scratch/stefan/7769621/working/building/REAL300000040533 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 629)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/629
`/scratch/stefan/7769621/working/3D/629' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC(C=NNC(=O)C2=CC=C(C)C=C2O)=CC=C1OCC(=O)[O-])

`REAL300000040533.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040533.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040533/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040533 none CCOC1=CC(C=NNC(=O)C2=CC=C(C)C=C2O)=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.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [90, 57, 19, 19, 19, 7, 7, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 84, 171, 188, 188, 90, 90, 90, 90, 90, 19, 7, 6, 1, 1, 2, 2, 2, 1, 2, 19, 19, 171, 171] 402
rigid atoms, others: [35, 36, 40, 9, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 41, 42, 43, 44, 45])
total number of confs: 811
number of broken/clashed sets: 127
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040533 none CCOC1=CC(C=NNC(=O)C2=CC=C(C)C=C2O)=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.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 9, 1, 1, 1, 1, 1, 7, 7, 8, 8, 7, 19, 19, 11, 19, 19, 19, 19, 1, 1, 1, 1, 9, 41, 76, 76, 31, 31, 31, 31, 31, 1, 7, 8, 19, 19, 19, 19, 19, 19, 38, 1, 1, 41, 41] 402
rigid atoms, others: [32, 2, 3, 4, 5, 6, 42, 43, 19, 20, 21, 22] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45])
total number of confs: 451
number of broken/clashed sets: 127
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040533 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040533
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040533/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040533
Building REAL300000040534
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040534'
/scratch/stefan/7769621/working/building/REAL300000040534 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040534

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040534/0 /scratch/stefan/7769621/working/building/REAL300000040534 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 630)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/630
`/scratch/stefan/7769621/working/3D/630' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CN(C3CCOCC3)N=C2C(=O)[O-])C(O)=C1)

`REAL300000040534.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040534.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040534/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040534 none CC1=CC=C(C(=O)NN=CC2=CN(C3CCOCC3)N=C2C(=O)[O-])C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [54, 41, 54, 54, 22, 22, 22, 13, 13, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 12, 12, 54, 54, 54, 54, 54, 54, 54, 54, 22, 13, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 108, 54] 108
rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 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, 44, 45])
total number of confs: 262
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: REAL300000040534 none CC1=CC=C(C(=O)NN=CC2=CN(C3CCOCC3)N=C2C(=O)[O-])C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [15, 11, 15, 15, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 1, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 9, 4, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 30, 15] 108
rigid atoms, others: [34, 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, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 93
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040534 none CC1=CC=C(C(=O)NN=CC2=CN(C3CCOCC3)N=C2C(=O)[O-])C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 14, 14, 15, 15, 15, 54, 54, 54, 54, 54, 15, 15, 15, 15, 15, 1, 1, 1, 2, 2, 2, 1, 1, 9, 14, 15, 54, 54, 54, 54, 54, 54, 54, 54, 54, 2, 1] 108
rigid atoms, others: [0, 1, 2, 3, 4, 5, 45, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 137
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040534 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040534
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040534/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040534
Building REAL300000040535
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040535'
/scratch/stefan/7769621/working/building/REAL300000040535 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040535

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040535/0 /scratch/stefan/7769621/working/building/REAL300000040535 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 631)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/631
`/scratch/stefan/7769621/working/3D/631' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C)C(C=NNC(=O)C2=CC=C(C)C=C2O)=C1C(=O)[O-])

`REAL300000040535.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040535.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040535/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040535 none COC1=CC=C(C)C(C=NNC(=O)C2=CC=C(C)C=C2O)=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.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.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, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
1  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: [56, 37, 37, 37, 37, 37, 37, 31, 31, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 56, 56, 56, 56, 56, 37, 37, 37, 37, 37, 31, 9, 1, 1, 2, 2, 2, 1, 2] 112
rigid atoms, others: [35, 36, 40, 11, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 41])
total number of confs: 182
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040535 none COC1=CC=C(C)C(C=NNC(=O)C2=CC=C(C)C=C2O)=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.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.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, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
1  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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 12, 12, 37, 37, 24, 37, 37, 37, 37, 1, 1, 3, 3, 3, 3, 3, 1, 1, 2, 2, 2, 3, 12, 37, 37, 37, 37, 37, 37, 74] 112
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 28, 29] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 204
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040535 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040535
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040535/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040535
Building REAL300000040536
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040536'
/scratch/stefan/7769621/working/building/REAL300000040536 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040536

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040536/0 /scratch/stefan/7769621/working/building/REAL300000040536 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 632)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/632
`/scratch/stefan/7769621/working/3D/632' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=C(C(=O)[O-])N(C)C3=CC=C(F)C=C32)C(O)=C1)

`REAL300000040536.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040536.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040536/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040536 none CC1=CC=C(C(=O)NN=CC2=C(C(=O)[O-])N(C)C3=CC=C(F)C=C32)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 11, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 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]
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, 13, 19, 19, 7, 7, 7, 4, 4, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 7, 4, 2, 2, 2, 1, 1, 1, 38, 19] 38
rigid atoms, others: [37, 38, 39, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41])
total number of confs: 99
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040536 none CC1=CC=C(C(=O)NN=CC2=C(C(=O)[O-])N(C)C3=CC=C(F)C=C32)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 11, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 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]
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: [1, 1, 1, 1, 1, 1, 10, 10, 10, 18, 18, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 2, 2, 2, 1, 1, 10, 18, 19, 19, 19, 19, 19, 19, 2, 1] 38
rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 43
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040536 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040536
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040536/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040536
Building REAL300000040537
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040537'
/scratch/stefan/7769621/working/building/REAL300000040537 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040537

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040537/0 /scratch/stefan/7769621/working/building/REAL300000040537 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 633)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/633
`/scratch/stefan/7769621/working/3D/633' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=C(C(=O)[O-])C2=CC=CC=C2S1)

`REAL300000040537.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040537.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040537/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040537 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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]
1  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 12, 12, 12, 34, 34, 25, 34, 34, 34, 34, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 34, 34, 34, 34, 34, 34, 67, 1, 1, 1, 1] 68
rigid atoms, others: [1, 37, 38, 39, 40, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 173
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040537 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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]
1  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [26, 26, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 26, 26, 10, 1, 1, 2, 2, 2, 1, 2, 34, 34, 34, 34] 68
rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 36, 37, 38, 39, 40])
total number of confs: 65
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040537 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040537
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040537/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040537
Building REAL300000040538
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040538'
/scratch/stefan/7769621/working/building/REAL300000040538 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040538

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040538/0 /scratch/stefan/7769621/working/building/REAL300000040538 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 634)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/634
`/scratch/stefan/7769621/working/3D/634' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=C(CCC(=O)[O-])O2)C(O)=C1)

`REAL300000040538.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040538.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040538/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040538 none CC1=CC=C(C(=O)NN=CC2=CC=C(CCC(=O)[O-])O2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
352  conformations in input
total number of sets (complete confs): 352
using faster count positions algorithm for large data
unique positions, atoms: [69, 48, 69, 69, 26, 26, 26, 8, 8, 1, 1, 1, 1, 1, 1, 8, 20, 29, 22, 1, 69, 69, 69, 69, 69, 69, 69, 69, 26, 8, 1, 1, 8, 8, 20, 20, 138, 69] 352
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])
total number of confs: 456
number of broken/clashed sets: 66
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040538 none CC1=CC=C(C(=O)NN=CC2=CC=C(CCC(=O)[O-])O2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
352  conformations in input
total number of sets (complete confs): 352
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 37, 37, 69, 69, 69, 69, 139, 176, 176, 173, 69, 1, 1, 1, 2, 2, 2, 1, 1, 10, 37, 69, 69, 139, 139, 176, 176, 2, 1] 352
rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 22, 26, 27, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 632
number of broken/clashed sets: 66
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040538 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040538
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040538/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040538
Building REAL300000040539
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040539'
/scratch/stefan/7769621/working/building/REAL300000040539 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040539

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040539/0 /scratch/stefan/7769621/working/building/REAL300000040539 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 635)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/635
`/scratch/stefan/7769621/working/3D/635' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=C(C(=O)[O-])C=C(Br)S2)C(O)=C1)

`REAL300000040539.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040539.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040539/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040539 none CC1=CC=C(C(=O)NN=CC2=C(C(=O)[O-])C=C(Br)S2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 17, 14, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 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: [21, 17, 21, 21, 10, 10, 10, 5, 5, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 9, 5, 1, 42, 21] 42
rigid atoms, others: [9, 10, 11, 12, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31])
total number of confs: 106
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040539 none CC1=CC=C(C(=O)NN=CC2=C(C(=O)[O-])C=C(Br)S2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 17, 14, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 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: [1, 1, 1, 1, 1, 1, 9, 9, 9, 16, 16, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 2, 2, 2, 1, 1, 9, 16, 21, 2, 1] 42
rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 25, 26, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30])
total number of confs: 47
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040539 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040539
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040539/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040539
Building REAL300000040540
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040540'
/scratch/stefan/7769621/working/building/REAL300000040540 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040540

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040540/0 /scratch/stefan/7769621/working/building/REAL300000040540 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 636)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/636
`/scratch/stefan/7769621/working/3D/636' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CNC3=C(C(=O)[O-])C=CC=C23)C(O)=C1)

`REAL300000040540.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040540.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040540/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040540 none CC1=CC=C(C(=O)NN=CC2=CNC3=C(C(=O)[O-])C=CC=C23)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 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]
1  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [33, 33, 33, 33, 17, 17, 17, 10, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 17, 10, 1, 1, 1, 1, 1, 66, 33] 66
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])
total number of confs: 134
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040540 none CC1=CC=C(C(=O)NN=CC2=CNC3=C(C(=O)[O-])C=CC=C23)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 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]
1  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 19, 19, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 2, 2, 2, 1, 1, 10, 19, 33, 33, 33, 33, 33, 2, 1] 66
rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 22, 23, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 68
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040540 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040540
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040540/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040540
Building REAL300000040541
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040541'
/scratch/stefan/7769621/working/building/REAL300000040541 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040541

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040541/0 /scratch/stefan/7769621/working/building/REAL300000040541 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 637)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/637
`/scratch/stefan/7769621/working/3D/637' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1)

`REAL300000040541.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040541.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040541/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040541 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 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]
1  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: [4, 1, 4, 4, 10, 10, 10, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 17, 17, 17, 17, 17, 17, 34, 1, 1, 1, 1, 1] 34
rigid atoms, others: [1, 38, 39, 40, 41, 42, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 74
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040541 none CC(=NNC(=O)C1=CC=C(C)C=C1O)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 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]
1  hydrogens need rotated
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [16, 16, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 16, 16, 16, 8, 1, 1, 2, 2, 2, 1, 2, 17, 17, 17, 17, 17] 34
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 11, 12, 13, 36, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 37, 38, 39, 40, 41, 42])
total number of confs: 41
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040541 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040541
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040541/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040541
Building REAL300000040542
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040542'
/scratch/stefan/7769621/working/building/REAL300000040542 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040542

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040542/0 /scratch/stefan/7769621/working/building/REAL300000040542 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 638)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/638
`/scratch/stefan/7769621/working/3D/638' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)C(O)=C1)

`REAL300000040542.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040542.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040542/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040542 none CC1=CC=C(C(=O)NN=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [31, 31, 31, 31, 18, 19, 19, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 19, 9, 1, 1, 1, 1, 62, 31] 62
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])
total number of confs: 138
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040542 none CC1=CC=C(C(=O)NN=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 21, 21, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 2, 2, 2, 1, 1, 10, 21, 31, 31, 31, 31, 2, 1] 62
rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 23, 24, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 62
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040542 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040542
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040542/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040542
Building REAL300000040543
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040543'
/scratch/stefan/7769621/working/building/REAL300000040543 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040543

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040543/0 /scratch/stefan/7769621/working/building/REAL300000040543 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 639)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/639
`/scratch/stefan/7769621/working/3D/639' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=CN3C(C(=O)[O-])=CN=C23)C(O)=C1)

`REAL300000040543.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040543.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040543/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040543 none CC1=CC=C(C(=O)NN=CC2=CC=CN3C(C(=O)[O-])=CN=C23)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 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]
1  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [16, 15, 16, 16, 7, 7, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 7, 3, 1, 1, 1, 1, 32, 16] 32
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])
total number of confs: 75
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040543 none CC1=CC=C(C(=O)NN=CC2=CC=CN3C(C(=O)[O-])=CN=C23)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 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]
1  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 2, 2, 2, 1, 1, 10, 16, 16, 16, 16, 16, 2, 1] 32
rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 23, 24, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 38
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040543 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040543
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040543/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040543
Building REAL300000040544
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040544'
/scratch/stefan/7769621/working/building/REAL300000040544 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040544

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040544/0 /scratch/stefan/7769621/working/building/REAL300000040544 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 640)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/640
`/scratch/stefan/7769621/working/3D/640' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=CC(F)=C2C(=O)[O-])C(O)=C1)

`REAL300000040544.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040544.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040544/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040544 none CC1=CC=C(C(=O)NN=CC2=CC=CC(F)=C2C(=O)[O-])C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 14, 14, 14, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 7, 5, 1, 1, 1, 28, 14] 28
rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 64
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040544 none CC1=CC=C(C(=O)NN=CC2=CC=CC(F)=C2C(=O)[O-])C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 6, 6, 6, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 2, 2, 2, 1, 1, 6, 8, 14, 14, 14, 2, 1] 28
rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 33
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040544 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040544
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040544/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040544
Building REAL300000040545
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040545'
/scratch/stefan/7769621/working/building/REAL300000040545 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040545

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040545/0 /scratch/stefan/7769621/working/building/REAL300000040545 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 641)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/641
`/scratch/stefan/7769621/working/3D/641' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)C(O)=C1)

`REAL300000040545.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040545.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040545/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040545 none CC1=CC=C(C(=O)NN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
172  conformations in input
total number of sets (complete confs): 172
using faster count positions algorithm for large data
unique positions, atoms: [86, 86, 86, 86, 70, 70, 70, 67, 67, 59, 59, 59, 59, 59, 59, 37, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 86, 86, 86, 86, 70, 67, 59, 59, 59, 59, 8, 8, 1, 1, 172, 86] 172
rigid atoms, others: [42, 43, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45])
total number of confs: 348
number of broken/clashed sets: 37
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040545 none CC1=CC=C(C(=O)NN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [17, 14, 17, 17, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 22, 59, 59, 59, 59, 59, 59, 59, 17, 17, 17, 17, 17, 17, 17, 17, 9, 5, 1, 1, 1, 1, 22, 22, 59, 59, 34, 17] 172
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, 44, 45])
total number of confs: 203
number of broken/clashed sets: 37
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040545 none CC1=CC=C(C(=O)NN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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, 1, 5, 5, 5, 9, 9, 17, 17, 17, 17, 17, 17, 36, 60, 86, 86, 86, 86, 86, 86, 86, 1, 1, 1, 2, 2, 2, 1, 1, 5, 9, 17, 17, 17, 17, 60, 60, 86, 86, 2, 1] 172
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 45, 26, 27, 28, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 215
number of broken/clashed sets: 37
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040545 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040545
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040545/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040545
Building REAL300000040546
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040546'
/scratch/stefan/7769621/working/building/REAL300000040546 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040546

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040546/0 /scratch/stefan/7769621/working/building/REAL300000040546 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 642)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/642
`/scratch/stefan/7769621/working/3D/642' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=CC(Br)=C2C(=O)[O-])C(O)=C1)

`REAL300000040546.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040546.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040546/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040546 none CC1=CC=C(C(=O)NN=CC2=CC=CC(Br)=C2C(=O)[O-])C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [10, 10, 10, 10, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 1, 1, 1, 20, 10] 20
rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 42
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040546 none CC1=CC=C(C(=O)NN=CC2=CC=CC(Br)=C2C(=O)[O-])C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 2, 2, 2, 1, 1, 6, 8, 10, 10, 10, 2, 1] 20
rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 29
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040546 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040546
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040546/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040546
Building REAL300000040547
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040547'
/scratch/stefan/7769621/working/building/REAL300000040547 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040547

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040547/0 /scratch/stefan/7769621/working/building/REAL300000040547 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 643)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/643
`/scratch/stefan/7769621/working/3D/643' -> `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=NNC(=O)C1=CC=C(C)C=C1O)

`REAL300000040547.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040547.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040547/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040547 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NNC(=O)C1=CC=C(C)C=C1O 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', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 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]
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, 58, 58, 58, 58, 58, 67, 58, 58, 58, 58, 58, 58, 59, 59, 26, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 68, 68, 68, 58, 67, 67, 67, 58, 58, 26, 9, 1, 1, 2, 2, 2, 1, 2] 136
rigid atoms, others: [40, 41, 45, 19, 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, 20, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 46])
total number of confs: 138
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040547 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NNC(=O)C1=CC=C(C)C=C1O 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', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 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]
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: [3, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 8, 8, 16, 16, 16, 58, 58, 36, 58, 58, 58, 58, 3, 3, 3, 1, 3, 3, 3, 1, 1, 8, 16, 58, 58, 58, 58, 58, 58, 116] 136
rigid atoms, others: [32, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 15, 16, 36, 37] set([0, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 308
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040547 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040547
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040547/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040547
Building REAL300000040548
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040548'
/scratch/stefan/7769621/working/building/REAL300000040548 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040548

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040548/0 /scratch/stefan/7769621/working/building/REAL300000040548 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 644)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/644
`/scratch/stefan/7769621/working/3D/644' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=C(C(=O)[O-])C=CC3=C2OCO3)C(O)=C1)

`REAL300000040548.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040548.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040548/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040548 none CC1=CC=C(C(=O)NN=CC2=C(C(=O)[O-])C=CC3=C2OCO3)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 12, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [25, 21, 25, 25, 11, 11, 11, 6, 6, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 11, 6, 1, 1, 1, 1, 50, 25] 50
rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37])
total number of confs: 127
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040548 none CC1=CC=C(C(=O)NN=CC2=C(C(=O)[O-])C=CC3=C2OCO3)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 12, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 2, 2, 2, 1, 1, 8, 13, 25, 25, 25, 25, 2, 1] 50
rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 23, 24, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 52
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040548 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040548
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040548/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040548
Building REAL300000040549
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040549'
/scratch/stefan/7769621/working/building/REAL300000040549 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040549

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040549/0 /scratch/stefan/7769621/working/building/REAL300000040549 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 645)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/645
`/scratch/stefan/7769621/working/3D/645' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC(C#N)=CC=C2C(=O)[O-])C(O)=C1)

`REAL300000040549.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040549.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040549/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040549 none CC1=CC=C(C(=O)NN=CC2=CC(C#N)=CC=C2C(=O)[O-])C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 18, 19, 19, 8, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 19, 19, 19, 19, 19, 19, 19, 19, 8, 6, 1, 1, 1, 38, 19] 38
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: 85
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040549 none CC1=CC=C(C(=O)NN=CC2=CC(C#N)=CC=C2C(=O)[O-])C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 7, 7, 7, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 2, 2, 2, 1, 1, 7, 9, 19, 19, 19, 2, 1] 38
rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 21, 22, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34])
total number of confs: 43
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040549 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040549/1 /scratch/stefan/7769621/working/building/REAL300000040549 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 646)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/646
`/scratch/stefan/7769621/working/3D/646' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC(C#N)=CC=C2C(=O)[O-])C([O-])=C1)

`REAL300000040549.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040549.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040549/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040549 none CC1=CC=C(C(=O)NN=CC2=CC(C#N)=CC=C2C(=O)[O-])C([O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
10  conformations in input
total number of sets (complete confs): 10
using default count positions algorithm for smaller data
unique positions, atoms: [10, 8, 10, 10, 8, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 8, 6, 1, 1, 1, 10] 10
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: 39
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040549 none CC1=CC=C(C(=O)NN=CC2=CC(C#N)=CC=C2C(=O)[O-])C([O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
10  conformations in input
total number of sets (complete confs): 10
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 2, 2, 2, 1, 1, 4, 6, 10, 10, 10, 1] 10
rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 21, 22, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33])
total number of confs: 25
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040549 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040549
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040549/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040549/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040549
Building REAL300000040550
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040550'
/scratch/stefan/7769621/working/building/REAL300000040550 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040550

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040550/0 /scratch/stefan/7769621/working/building/REAL300000040550 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 647)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/647
`/scratch/stefan/7769621/working/3D/647' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)C(O)=C1)

`REAL300000040550.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040550.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040550/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040550 none CC1=CC=C(C(=O)NN=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 4, 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: [64, 37, 64, 64, 24, 24, 24, 8, 8, 1, 1, 1, 1, 1, 1, 8, 36, 53, 53, 1, 1, 1, 64, 64, 64, 64, 64, 64, 64, 64, 24, 8, 1, 1, 36, 36, 1, 128, 64] 402
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])
total number of confs: 503
number of broken/clashed sets: 83
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040550 none CC1=CC=C(C(=O)NN=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 4, 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, 11, 11, 10, 25, 26, 64, 64, 41, 64, 156, 201, 201, 201, 64, 64, 64, 1, 1, 1, 2, 2, 2, 1, 1, 11, 26, 64, 64, 201, 201, 64, 2, 1] 402
rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 22, 23, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 569
number of broken/clashed sets: 83
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040550 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040550
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040550/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040550
Building REAL300000040551
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040551'
/scratch/stefan/7769621/working/building/REAL300000040551 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040551

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040551/0 /scratch/stefan/7769621/working/building/REAL300000040551 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 648)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/648
`/scratch/stefan/7769621/working/3D/648' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)C(O)=C1)

`REAL300000040551.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040551.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040551/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040551 none CC1=CC=C(C(=O)NN=CC2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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]
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: [12, 8, 12, 12, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 13, 13, 13, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 6, 4, 1, 1, 9, 13, 13, 1, 1, 24, 12] 72
rigid atoms, others: [34, 35, 39, 40, 9, 10, 11, 12, 13, 14, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 41, 42])
total number of confs: 109
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040551 none CC1=CC=C(C(=O)NN=CC2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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]
1  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 8, 8, 12, 12, 8, 8, 22, 22, 22, 32, 36, 36, 36, 12, 12, 1, 1, 1, 2, 2, 2, 1, 1, 6, 8, 12, 12, 32, 36, 36, 12, 12, 2, 1] 72
rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 165
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040551 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040551
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040551/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040551
Building REAL300000040552
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040552'
/scratch/stefan/7769621/working/building/REAL300000040552 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040552

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040552/0 /scratch/stefan/7769621/working/building/REAL300000040552 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 649)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/649
`/scratch/stefan/7769621/working/3D/649' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NSC(C=NNC(=O)C2=CC=C(C)C=C2O)=C1C(=O)[O-])

`REAL300000040552.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040552.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040552/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040552 none CC1=NSC(C=NNC(=O)C2=CC=C(C)C=C2O)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [20, 20, 20, 20, 15, 15, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 15, 9, 1, 1, 2, 2, 2, 1, 2] 40
rigid atoms, others: [32, 8, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 33])
total number of confs: 43
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040552 none CC1=NSC(C=NNC(=O)C2=CC=C(C)C=C2O)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9, 20, 20, 15, 20, 20, 20, 20, 1, 1, 3, 3, 2, 2, 2, 6, 9, 20, 20, 20, 20, 20, 20, 40] 40
rigid atoms, others: [0, 1, 2, 3, 4, 5, 18, 19] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 106
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040552 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040552
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040552/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040552
Building REAL300000040553
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040553'
/scratch/stefan/7769621/working/building/REAL300000040553 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040553

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040553/0 /scratch/stefan/7769621/working/building/REAL300000040553 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 650)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/650
`/scratch/stefan/7769621/working/3D/650' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)C(O)=C1)

`REAL300000040553.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040553.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040553/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040553 none CC1=CC=C(C(=O)NN=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [33, 33, 33, 33, 21, 21, 21, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 21, 10, 1, 1, 1, 66, 33] 66
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, 36, 37, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 143
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040553 none CC1=CC=C(C(=O)NN=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 17, 17, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 2, 2, 2, 1, 1, 9, 17, 33, 33, 33, 2, 1] 66
rigid atoms, others: [0, 1, 2, 3, 4, 5, 23, 24, 25, 29, 30, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36])
total number of confs: 65
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040553 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040553
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040553/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040553
Building REAL300000040554
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040554'
/scratch/stefan/7769621/working/building/REAL300000040554 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040554

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040554/0 /scratch/stefan/7769621/working/building/REAL300000040554 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 651)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/651
`/scratch/stefan/7769621/working/3D/651' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=NNC(=O)C1=CC=C(C)C=C1O)

`REAL300000040554.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040554.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040554/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040554 none COC1=CC(C(=O)[O-])=CC=C1C=NNC(=O)C1=CC=C(C)C=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 13, 13, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 13, 8, 1, 1, 2, 2, 2, 1, 2] 64
rigid atoms, others: [32, 33, 37, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 38])
total number of confs: 60
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040554 none COC1=CC(C(=O)[O-])=CC=C1C=NNC(=O)C1=CC=C(C)C=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 8, 14, 14, 14, 32, 32, 31, 32, 32, 32, 32, 3, 3, 3, 1, 1, 1, 8, 14, 32, 32, 32, 32, 32, 32, 64] 64
rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 11, 27, 28, 29] set([0, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 139
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040554 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040554
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040554/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040554
Building REAL300000040555
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040555'
/scratch/stefan/7769621/working/building/REAL300000040555 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040555

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040555/0 /scratch/stefan/7769621/working/building/REAL300000040555 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 652)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/652
`/scratch/stefan/7769621/working/3D/652' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)C(O)=C1)

`REAL300000040555.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040555.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040555/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040555 none CC1=CC=C(C(=O)NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 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]
1  hydrogens need rotated
322  conformations in input
total number of sets (complete confs): 322
using faster count positions algorithm for large data
unique positions, atoms: [161, 143, 161, 161, 81, 81, 81, 40, 40, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 13, 13, 161, 161, 161, 161, 161, 161, 161, 161, 81, 40, 1, 1, 1, 1, 13, 13, 322, 161] 322
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])
total number of confs: 742
number of broken/clashed sets: 56
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040555 none CC1=CC=C(C(=O)NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 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]
1  hydrogens need rotated
322  conformations in input
total number of sets (complete confs): 322
using faster count positions algorithm for large data
unique positions, atoms: [58, 32, 58, 58, 20, 20, 20, 8, 8, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 25, 25, 13, 1, 1, 58, 58, 58, 58, 58, 58, 58, 58, 20, 8, 13, 13, 13, 13, 1, 1, 116, 58] 322
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])
total number of confs: 375
number of broken/clashed sets: 56
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040555 none CC1=CC=C(C(=O)NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 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]
1  hydrogens need rotated
322  conformations in input
total number of sets (complete confs): 322
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 11, 11, 37, 37, 58, 58, 58, 161, 161, 161, 161, 161, 161, 161, 161, 58, 58, 1, 1, 1, 2, 2, 2, 1, 1, 11, 37, 161, 161, 161, 161, 58, 58, 2, 1] 322
rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 376
number of broken/clashed sets: 56
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040555 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040555
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040555/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040555
Building REAL300000040556
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040556'
/scratch/stefan/7769621/working/building/REAL300000040556 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040556

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040556/0 /scratch/stefan/7769621/working/building/REAL300000040556 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 653)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/653
`/scratch/stefan/7769621/working/3D/653' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=CC=C1C=NNC1=CC=CC2=C1CCCC2)

`REAL300000040556.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040556.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040556/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040556 none O=C([O-])COC1=CC=CC=C1C=NNC1=CC=CC2=C1CCCC2 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.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: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
162  conformations in input
total number of sets (complete confs): 162
using faster count positions algorithm for large data
unique positions, atoms: [162, 162, 162, 126, 59, 59, 59, 33, 59, 59, 33, 33, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 162, 162, 59, 59, 59, 59, 33, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 162
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 500
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040556 none O=C([O-])COC1=CC=CC=C1C=NNC1=CC=CC2=C1CCCC2 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.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: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [64, 41, 64, 10, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 20, 59, 59, 59, 59, 59, 59, 59, 59, 59, 41, 41, 1, 1, 1, 1, 4, 20, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59] 162
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28, 29] set([0, 1, 2, 3, 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])
total number of confs: 299
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040556 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040556
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040556/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040556
Building REAL300000040557
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040557'
/scratch/stefan/7769621/working/building/REAL300000040557 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040557

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040557/0 /scratch/stefan/7769621/working/building/REAL300000040557 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 654)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/654
`/scratch/stefan/7769621/working/3D/654' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=CC3=C2CCCC3)C=C1)

`REAL300000040557.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040557.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040557/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040557 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC3=C2CCCC3)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.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']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [2, 7, 2, 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]
0  hydrogens need rotated
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, 132, 55, 33, 83, 82, 32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 83, 83, 201, 201, 83, 82, 32, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 83, 83] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 42, 41, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 736
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040557 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC3=C2CCCC3)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.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']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [2, 7, 2, 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]
0  hydrogens 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, 15, 30, 3, 1, 1, 1, 1, 1, 1, 7, 7, 39, 82, 82, 82, 82, 82, 82, 83, 83, 82, 1, 1, 15, 15, 1, 1, 7, 39, 82, 82, 82, 82, 82, 83, 83, 83, 83, 82, 82, 1, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 42, 41, 22, 23, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 249
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040557 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040557
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040557/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040557
Building REAL300000040558
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040558'
/scratch/stefan/7769621/working/building/REAL300000040558 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040558

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040558/0 /scratch/stefan/7769621/working/building/REAL300000040558 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 655)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/655
`/scratch/stefan/7769621/working/3D/655' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=CC(C=NNC2=CC=CC3=C2CCCC3)=C1)C(=O)[O-])

`REAL300000040558.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040558.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040558/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040558 none CC(OC1=CC=CC(C=NNC2=CC=CC3=C2CCCC3)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [7, 7, 3, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 174, 62, 62, 62, 62, 62, 28, 28, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 62, 201, 201, 201, 201, 201, 201, 201, 62, 62, 62, 28, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 62] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 45])
total number of confs: 405
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040558 none CC(OC1=CC=CC(C=NNC2=CC=CC3=C2CCCC3)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [7, 7, 3, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 23, 62, 62, 62, 62, 62, 62, 62, 62, 62, 1, 30, 45, 45, 30, 30, 30, 30, 1, 1, 1, 7, 23, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 1] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 45, 21, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 264
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040558 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040558
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040558/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040558
Building REAL300000040559
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040559'
/scratch/stefan/7769621/working/building/REAL300000040559 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040559

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040559/0 /scratch/stefan/7769621/working/building/REAL300000040559 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 656)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/656
`/scratch/stefan/7769621/working/3D/656' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=CC(C=NNC2=CC=CC3=C2CCCC3)=C1)

`REAL300000040559.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040559.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040559/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040559 none O=C([O-])CCOC1=CC=CC(C=NNC2=CC=CC3=C2CCCC3)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', '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.ar', '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']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 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: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 191, 143, 53, 53, 53, 53, 53, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 201, 201, 191, 191, 53, 53, 53, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53] 201
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 45])
total number of confs: 507
number of broken/clashed sets: 24
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040559 none O=C([O-])CCOC1=CC=CC(C=NNC2=CC=CC3=C2CCCC3)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', '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.ar', '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']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 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: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 34, 45, 23, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 23, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 34, 34, 23, 23, 1, 1, 1, 7, 23, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1] 201
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 45, 24, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 282
number of broken/clashed sets: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040559 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040559
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040559/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040559
Building REAL300000040560
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040560'
/scratch/stefan/7769621/working/building/REAL300000040560 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040560

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040560/0 /scratch/stefan/7769621/working/building/REAL300000040560 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 657)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/657
`/scratch/stefan/7769621/working/3D/657' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=CC3=C2CCCC3)C=C1[N+](=O)[O-])

`REAL300000040560.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040560.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040560/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040560 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC3=C2CCCC3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [31, 31, 31, 31, 26, 16, 26, 26, 10, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 31, 31, 26, 26, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26] 31
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 44])
total number of confs: 94
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040560 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC3=C2CCCC3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 7, 7, 16, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 2, 2, 5, 5, 1, 1, 7, 16, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1] 31
rigid atoms, others: [4, 5, 6, 7, 8, 9, 44, 22, 23, 24, 29, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 80
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040560 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040560
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040560/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040560
Building REAL300000040561
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040561'
/scratch/stefan/7769621/working/building/REAL300000040561 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040561

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040561/0 /scratch/stefan/7769621/working/building/REAL300000040561 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 658)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/658
`/scratch/stefan/7769621/working/3D/658' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=CC(C=NNC2=CC=CC3=C2CCCC3)=C1)

`REAL300000040561.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040561.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040561/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040561 none O=C([O-])COC1=CC=CC(C=NNC2=CC=CC3=C2CCCC3)=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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 135, 55, 55, 55, 55, 55, 28, 28, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 201, 201, 55, 55, 55, 28, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55] 201
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 42, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 556
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040561 none O=C([O-])COC1=CC=CC(C=NNC2=CC=CC3=C2CCCC3)=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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [42, 23, 42, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 24, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 23, 23, 1, 1, 1, 7, 24, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 23, 26, 27, 28, 42] set([0, 1, 2, 3, 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])
total number of confs: 234
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040561 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040561
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040561/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040561
Building REAL300000040562
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040562'
/scratch/stefan/7769621/working/building/REAL300000040562 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040562

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040562/0 /scratch/stefan/7769621/working/building/REAL300000040562 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 659)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/659
`/scratch/stefan/7769621/working/3D/659' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNC2=CC=CC3=C2CCCC3)C(OCC(=O)[O-])=C1)

`REAL300000040562.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040562.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040562/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040562 none COC1=CC=C(C=NNC2=CC=CC3=C2CCCC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [63, 42, 29, 42, 42, 29, 29, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 108, 201, 201, 201, 42, 63, 63, 63, 42, 42, 29, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 42] 201
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 44, 45, 46])
total number of confs: 677
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040562 none COC1=CC=C(C=NNC2=CC=CC3=C2CCCC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 4, 16, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 8, 37, 66, 66, 1, 3, 3, 3, 1, 1, 4, 16, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 37, 37, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 46, 19, 20, 25, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 294
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040562 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040562
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040562/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040562
Building REAL300000040563
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040563'
/scratch/stefan/7769621/working/building/REAL300000040563 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040563

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040563/0 /scratch/stefan/7769621/working/building/REAL300000040563 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 660)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/660
`/scratch/stefan/7769621/working/3D/660' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=CC3=C2CCCC3)C=C1)

`REAL300000040563.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040563.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040563/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040563 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=CC3=C2CCCC3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', '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.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']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 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]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 200, 201, 112, 200, 200, 34, 20, 55, 54, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 54, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55] 201
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 42, 41, 24, 25, 26, 27, 28, 29])
total number of confs: 730
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040563 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=CC3=C2CCCC3)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', '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.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']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 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]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 31, 49, 7, 31, 31, 1, 1, 1, 1, 1, 1, 6, 6, 27, 54, 54, 54, 54, 54, 54, 55, 55, 54, 1, 1, 1, 1, 6, 27, 54, 54, 54, 54, 54, 55, 55, 55, 55, 54, 54, 1, 1] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 41, 24, 25, 26, 27, 42] set([0, 1, 2, 3, 4, 5, 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: 274
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040563 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040563
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040563/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040563
Building REAL300000040564
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040564'
/scratch/stefan/7769621/working/building/REAL300000040564 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040564

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040564/0 /scratch/stefan/7769621/working/building/REAL300000040564 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 661)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/661
`/scratch/stefan/7769621/working/3D/661' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=CC2=C1CCCC2)

`REAL300000040564.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040564.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040564/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040564 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=CC2=C1CCCC2 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.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']
dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 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]
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, 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, 59, 59, 59, 59, 59, 59, 59, 38, 38, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 38, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 59
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28])
total number of confs: 92
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040564 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=CC2=C1CCCC2 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.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']
dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 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]
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, 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, 2, 2, 1, 1, 1, 1, 1, 11, 11, 41, 59, 59, 59, 59, 59, 59, 59, 59, 59, 2, 2, 2, 1, 11, 41, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59] 59
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 26] set([4, 5, 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])
total number of confs: 140
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040564 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040564
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040564/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040564
Building REAL300000040565
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040565'
/scratch/stefan/7769621/working/building/REAL300000040565 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040565

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040565/0 /scratch/stefan/7769621/working/building/REAL300000040565 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 662)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/662
`/scratch/stefan/7769621/working/3D/662' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=CC3=C2CCCC3)C=C1)

`REAL300000040565.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040565.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040565/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040565 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=CC3=C2CCCC3)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.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']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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]
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, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 46, 46, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 77, 77, 77, 77, 77, 77, 46, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 77, 77] 77
rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 44, 45])
total number of confs: 122
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040565 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=CC3=C2CCCC3)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.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']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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]
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, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 10, 10, 36, 77, 77, 77, 77, 77, 77, 77, 77, 77, 1, 1, 4, 4, 4, 1, 10, 36, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 1, 1] 77
rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 45, 44, 25, 26, 30] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 150
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040565 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040565
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040565/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040565
Building REAL300000040566
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040566'
/scratch/stefan/7769621/working/building/REAL300000040566 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040566

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040566/0 /scratch/stefan/7769621/working/building/REAL300000040566 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 663)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/663
`/scratch/stefan/7769621/working/3D/663' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=NNC(C=NNC3=CC=CC4=C3CCCC4)=C2C=C1)

`REAL300000040566.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040566.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040566/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040566 none O=C([O-])C1=CC2=NNC(C=NNC3=CC=CC4=C3CCCC4)=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 39, 39, 36, 36, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 36, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39] 39
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 40, 41, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 61
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040566 none O=C([O-])C1=CC2=NNC(C=NNC3=CC=CC4=C3CCCC4)=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 6, 19, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1] 39
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 40, 41, 22, 23, 24, 25, 26] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 75
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040566 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040566/1 /scratch/stefan/7769621/working/building/REAL300000040566 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 664)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/664
`/scratch/stefan/7769621/working/3D/664' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(=C1)NN=C2C=NNC1=CC=CC2=C1CCCC2)

`REAL300000040566.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040566.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040566/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040566 none O=C([O-])C1=CC=C2C(=C1)NN=C2C=NNC1=CC=CC2=C1CCCC2 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', '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', 'C.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, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 6, 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, 7, 4, 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]
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, 84, 85, 84, 84, 84, 84, 85, 85, 85, 85, 51, 51, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 84, 84, 85, 85, 51, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 85
rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30])
total number of confs: 135
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040566 none O=C([O-])C1=CC=C2C(=C1)NN=C2C=NNC1=CC=CC2=C1CCCC2 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', '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', 'C.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, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 6, 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, 7, 4, 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]
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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 37, 84, 84, 84, 84, 84, 84, 85, 84, 84, 1, 1, 1, 1, 10, 37, 84, 85, 84, 84, 84, 85, 85, 85, 85, 84, 84] 85
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28] set([0, 2, 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: 170
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040566 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040566
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040566/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040566/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040566
Building REAL300000040567
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040567'
/scratch/stefan/7769621/working/building/REAL300000040567 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040567

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040567/0 /scratch/stefan/7769621/working/building/REAL300000040567 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 665)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/665
`/scratch/stefan/7769621/working/3D/665' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=CC=CC3=C2CCCC3)=C([N+](=O)[O-])C=C1OCC(=O)[O-])

`REAL300000040567.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040567.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040567/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040567 none COC1=CC(C=NNC2=CC=CC3=C2CCCC3)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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]
0  hydrogens 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, 66, 66, 66, 32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 66, 66, 168, 200, 201, 201, 109, 109, 109, 66, 32, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 200, 200] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 46, 47, 48])
total number of confs: 513
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040567 none COC1=CC(C=NNC2=CC=CC3=C2CCCC3)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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]
0  hydrogens 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, 66, 66, 66, 66, 66, 66, 66, 66, 66, 1, 1, 2, 2, 1, 1, 1, 9, 17, 25, 25, 3, 3, 3, 1, 7, 23, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 1, 17, 17] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 46, 18, 19, 22, 23, 24] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48])
total number of confs: 199
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040567 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040567
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040567/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040567
Building REAL300000040568
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040568'
/scratch/stefan/7769621/working/building/REAL300000040568 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040568

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040568/0 /scratch/stefan/7769621/working/building/REAL300000040568 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 666)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/666
`/scratch/stefan/7769621/working/3D/666' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=CC=CC3=C2CCCC3)=CC=C1OCCC(=O)[O-])

`REAL300000040568.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040568.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040568/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040568 none COC1=CC(C=NNC2=CC=CC3=C2CCCC3)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [7, 3, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 47, 47, 47, 14, 13, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 139, 189, 189, 201, 193, 81, 81, 81, 47, 13, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 189, 189, 189, 189] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 44, 45, 46, 47, 48, 49])
total number of confs: 550
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040568 none COC1=CC(C=NNC2=CC=CC3=C2CCCC3)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [7, 3, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 9, 34, 37, 55, 50, 4, 4, 4, 1, 7, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 34, 34, 36, 36] 201
rigid atoms, others: [1, 2, 3, 4, 5, 44, 45, 18, 19, 20, 21, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 49])
total number of confs: 286
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040568 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040568
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040568/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040568
Building REAL300000040569
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040569'
/scratch/stefan/7769621/working/building/REAL300000040569 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040569

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040569/0 /scratch/stefan/7769621/working/building/REAL300000040569 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 667)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/667
`/scratch/stefan/7769621/working/3D/667' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=CC3=C2CCCC3)C(Cl)=C1)

`REAL300000040569.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040569.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040569/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040569 none O=C([O-])C1=CC=C(C=NNC2=CC=CC3=C2CCCC3)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', '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.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 16, 1, 7, 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, 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]
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, 35, 41, 41, 34, 34, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 34, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41] 41
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 38])
total number of confs: 91
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040569 none O=C([O-])C1=CC=C(C=NNC2=CC=CC3=C2CCCC3)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', '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.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 16, 1, 7, 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, 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]
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, 8, 8, 26, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 8, 26, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1] 41
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 38] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 89
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040569 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040569
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040569/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040569
Building REAL300000040570
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040570'
/scratch/stefan/7769621/working/building/REAL300000040570 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040570

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040570/0 /scratch/stefan/7769621/working/building/REAL300000040570 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 668)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/668
`/scratch/stefan/7769621/working/3D/668' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C=NNC2=CC=CC3=C2CCCC3)=CC=C1O)

`REAL300000040570.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040570.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040570/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040570 none O=C([O-])C1=CC(C=NNC2=CC=CC3=C2CCCC3)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', '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.3', 'C.3', 'C.3', 'C.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', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 6, 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, 4, 7, 7, 7, 7, 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]
1  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [57, 57, 57, 57, 57, 39, 39, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 39, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 114] 114
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 1, 2, 3, 4, 5, 6, 7, 39, 19, 20, 21, 22, 23, 24, 25, 38, 37])
total number of confs: 202
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040570 none O=C([O-])C1=CC(C=NNC2=CC=CC3=C2CCCC3)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', '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.3', 'C.3', 'C.3', 'C.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', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 6, 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, 4, 7, 7, 7, 7, 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]
1  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 8, 32, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 8, 32, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 2] 114
rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 38, 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, 36, 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/7769621/working/building/REAL300000040570 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040570
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040570/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040570
Building REAL300000040571
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040571'
/scratch/stefan/7769621/working/building/REAL300000040571 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040571

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040571/0 /scratch/stefan/7769621/working/building/REAL300000040571 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 669)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/669
`/scratch/stefan/7769621/working/3D/669' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=C(C=NNC2=CC=CC3=C2CCCC3)C=C1)C(=O)[O-])

`REAL300000040571.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040571.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040571/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040571 none CC(OC1=CC=C(C=NNC2=CC=CC3=C2CCCC3)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.ar', 'C.ar', '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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [7, 7, 3, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 162, 62, 35, 97, 96, 35, 34, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 97, 97, 201, 201, 201, 201, 201, 201, 201, 97, 96, 34, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 97, 97] 201
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 44, 45])
total number of confs: 688
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040571 none CC(OC1=CC=C(C=NNC2=CC=CC3=C2CCCC3)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.ar', 'C.ar', '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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [7, 7, 3, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 6, 1, 1, 1, 1, 1, 1, 7, 7, 43, 96, 96, 96, 96, 96, 97, 97, 97, 97, 1, 1, 16, 24, 24, 16, 16, 16, 16, 1, 1, 7, 43, 96, 96, 96, 97, 97, 97, 97, 97, 97, 97, 96, 1, 1] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 44, 45, 20, 21, 29, 30] set([0, 1, 8, 9, 10, 11, 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, 42, 43])
total number of confs: 253
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040571 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040571
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040571/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040571
Building REAL300000040572
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040572'
/scratch/stefan/7769621/working/building/REAL300000040572 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040572

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040572/0 /scratch/stefan/7769621/working/building/REAL300000040572 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 670)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/670
`/scratch/stefan/7769621/working/3D/670' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CN1C=C(C=NNC2=CC=CC3=C2CCCC3)C2=CC=CC=C21)

`REAL300000040572.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040572.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040572/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040572 none O=C([O-])CN1C=C(C=NNC2=CC=CC3=C2CCCC3)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.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: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 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, 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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 123, 123, 123, 41, 41, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 123, 123, 123, 201, 201, 123, 41, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 123] 201
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 42, 43, 44, 45])
total number of confs: 597
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040572 none O=C([O-])CN1C=C(C=NNC2=CC=CC3=C2CCCC3)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.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: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 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, 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, 7]
0  hydrogens 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, 8, 15, 1, 1, 1, 1, 1, 10, 10, 55, 123, 123, 123, 123, 123, 123, 123, 123, 123, 1, 1, 1, 1, 1, 1, 8, 8, 1, 10, 54, 123, 123, 123, 123, 123, 123, 123, 123, 123, 123, 123, 1, 1, 1, 1] 201
rigid atoms, others: [3, 4, 5, 6, 7, 42, 43, 44, 45, 20, 21, 22, 23, 24, 25, 28] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 270
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040572 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040572
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040572/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040572
Building REAL300000040573
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040573'
/scratch/stefan/7769621/working/building/REAL300000040573 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040573

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040573/0 /scratch/stefan/7769621/working/building/REAL300000040573 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 671)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/671
`/scratch/stefan/7769621/working/3D/671' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC2=C1CCCC2)C1=CC=CC(OCCCC(=O)[O-])=C1)

`REAL300000040573.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040573.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040573/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040573 none CC(=NNC1=CC=CC2=C1CCCC2)C1=CC=CC(OCCCC(=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.ar', 'C.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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]
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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 18, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 7, 24, 35, 52, 71, 71, 1, 9, 9, 9, 18, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 24, 24, 35, 35, 52, 52, 1] 201
rigid atoms, others: [1, 51, 42, 43, 44, 14, 15, 16, 17, 18, 19, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47, 48, 49, 50])
total number of confs: 361
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040573 none CC(=NNC1=CC=CC2=C1CCCC2)C1=CC=CC(OCCCC(=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.ar', 'C.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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]
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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 32, 32, 32, 32, 32, 91, 142, 159, 201, 201, 201, 32, 9, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 142, 142, 159, 159, 201, 201, 32] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 712
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040573 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040573
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040573/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040573
Building REAL300000040574
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040574'
/scratch/stefan/7769621/working/building/REAL300000040574 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040574

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040574/0 /scratch/stefan/7769621/working/building/REAL300000040574 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 672)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/672
`/scratch/stefan/7769621/working/3D/672' -> `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=NC1=CC=CC2=C1CCCC2)

`REAL300000040574.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040574.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040574/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040574 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=CC2=C1CCCC2 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.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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, 7]
0  hydrogens 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, 4, 22, 46, 49, 49, 49, 49, 49, 163, 201, 201, 201, 201, 49, 49, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 47, 47, 49, 49, 49, 49, 201, 201, 201, 201, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 574
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040574 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=CC2=C1CCCC2 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.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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, 7]
0  hydrogens 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, 3, 2, 1, 1, 1, 1, 1, 1, 11, 25, 25, 31, 31, 1, 1, 8, 32, 32, 49, 49, 49, 49, 49, 49, 49, 49, 49, 8, 8, 8, 8, 3, 3, 2, 2, 1, 1, 25, 25, 25, 25, 1, 1, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 201
rigid atoms, others: [3, 36, 5, 6, 7, 8, 42, 43, 14, 15, 4, 37] 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, 33, 34, 35, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 185
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040574 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040574
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040574/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040574
Building REAL300000040575
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040575'
/scratch/stefan/7769621/working/building/REAL300000040575 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040575

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040575/0 /scratch/stefan/7769621/working/building/REAL300000040575 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 673)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/673
`/scratch/stefan/7769621/working/3D/673' -> `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=NC1=CC=CC2=C1CCCC2)

`REAL300000040575.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040575.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040575/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040575 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=CC2=C1CCCC2 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.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, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 4, 23, 47, 53, 53, 53, 53, 53, 136, 201, 201, 201, 53, 53, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 51, 51, 51, 53, 53, 53, 201, 201, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 672
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040575 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=CC2=C1CCCC2 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.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, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 3, 2, 1, 1, 1, 1, 1, 1, 6, 18, 25, 25, 1, 1, 9, 41, 41, 53, 53, 53, 53, 53, 53, 53, 53, 53, 9, 9, 9, 9, 3, 3, 2, 2, 1, 1, 18, 18, 1, 1, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53] 201
rigid atoms, others: [35, 4, 5, 6, 7, 8, 39, 13, 14, 40, 3, 36] 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, 32, 33, 34, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 175
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040575 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040575
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040575/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040575
Building REAL300000040576
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040576'
/scratch/stefan/7769621/working/building/REAL300000040576 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040576

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040576/0 /scratch/stefan/7769621/working/building/REAL300000040576 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 674)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/674
`/scratch/stefan/7769621/working/3D/674' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC2=C1CCCC2)C1=CC=CC(OC(C)C(=O)[O-])=C1)

`REAL300000040576.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040576.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040576/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040576 none CC(=NNC1=CC=CC2=C1CCCC2)C1=CC=CC(OC(C)C(=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.ar', 'C.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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]
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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 24, 59, 59, 59, 59, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 1, 11, 27, 27, 39, 39, 1, 9, 9, 9, 24, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 1, 1, 1, 27, 27, 27, 27, 1] 201
rigid atoms, others: [1, 48, 41, 42, 43, 14, 15, 16, 17, 18, 19, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47])
total number of confs: 237
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040576 none CC(=NNC1=CC=CC2=C1CCCC2)C1=CC=CC(OC(C)C(=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.ar', 'C.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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]
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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 22, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 59, 59, 59, 59, 59, 180, 201, 201, 201, 201, 59, 22, 22, 22, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 201, 201, 201, 201, 59] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 380
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040576 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040576
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040576/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040576
Building REAL300000040577
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040577'
/scratch/stefan/7769621/working/building/REAL300000040577 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040577

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040577/0 /scratch/stefan/7769621/working/building/REAL300000040577 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 675)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/675
`/scratch/stefan/7769621/working/3D/675' -> `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=NC1=CC=CC2=C1CCCC2)

`REAL300000040577.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040577.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040577/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040577 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=CC2=C1CCCC2 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.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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, 7]
0  hydrogens 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, 4, 24, 45, 51, 53, 53, 51, 53, 183, 201, 201, 201, 201, 53, 53, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 47, 47, 51, 51, 53, 53, 201, 201, 201, 201, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 500
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040577 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=CC2=C1CCCC2 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.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 5, 4, 1, 1, 1, 1, 1, 1, 6, 16, 16, 23, 23, 1, 1, 10, 34, 34, 53, 53, 53, 53, 53, 53, 53, 53, 53, 10, 10, 10, 10, 5, 5, 4, 4, 1, 1, 16, 16, 16, 16, 1, 1, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53] 201
rigid atoms, others: [3, 36, 5, 6, 7, 8, 42, 43, 14, 15, 4, 37] 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, 33, 34, 35, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 174
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040577 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040577
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040577/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040577
Building REAL300000040578
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040578'
/scratch/stefan/7769621/working/building/REAL300000040578 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040578

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040578/0 /scratch/stefan/7769621/working/building/REAL300000040578 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 676)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/676
`/scratch/stefan/7769621/working/3D/676' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC1=CC=CC2=C1CCCC2)C1=CC=C(OCCCCC(=O)[O-])C=C1)

`REAL300000040578.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040578.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040578/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040578 none CCC(=NNC1=CC=CC2=C1CCCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 17, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 6, 7, 19, 21, 34, 41, 41, 1, 1, 9, 9, 9, 9, 9, 17, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 7, 7, 19, 19, 21, 21, 34, 34, 1, 1] 201
rigid atoms, others: [2, 27, 46, 15, 16, 17, 18, 19, 56, 57, 47, 28] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50, 51, 52, 53, 54, 55])
total number of confs: 257
number of broken/clashed sets: 57
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040578 none CCC(=NNC1=CC=CC2=C1CCCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 34, 34, 12, 12, 66, 97, 146, 148, 176, 199, 199, 34, 34, 19, 19, 19, 18, 18, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 97, 97, 146, 146, 148, 148, 176, 176, 34, 34] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57])
total number of confs: 858
number of broken/clashed sets: 57
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040578 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040578
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040578/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040578
Building REAL300000040579
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040579'
/scratch/stefan/7769621/working/building/REAL300000040579 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040579

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040579/0 /scratch/stefan/7769621/working/building/REAL300000040579 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 677)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/677
`/scratch/stefan/7769621/working/3D/677' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC2=C1CCCC2)C1=CSC(C(=O)[O-])=C1)

`REAL300000040579.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040579.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040579/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040579 none CC(=NNC1=CC=CC2=C1CCCC2)C1=CSC(C(=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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 14, 1, 1, 11, 11, 1, 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]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 12, 12, 35, 71, 71, 71, 71, 71, 71, 71, 71, 71, 1, 1, 1, 1, 1, 2, 2, 1, 12, 12, 12, 35, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 1, 1] 71
rigid atoms, others: [1, 37, 38, 14, 15, 16, 17, 18, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 144
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040579 none CC(=NNC1=CC=CC2=C1CCCC2)C1=CSC(C(=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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 14, 1, 1, 11, 11, 1, 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]
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: [42, 42, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 71, 71, 71, 71, 71, 71, 71, 42, 42, 42, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 71, 71] 71
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 1, 2, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25])
total number of confs: 108
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040579 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040579
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040579/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040579
Building REAL300000040580
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040580'
/scratch/stefan/7769621/working/building/REAL300000040580 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040580

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040580/0 /scratch/stefan/7769621/working/building/REAL300000040580 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 678)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/678
`/scratch/stefan/7769621/working/3D/678' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=CC3=C2CCCC3)C1)

`REAL300000040580.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040580.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040580/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040580 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=CC3=C2CCCC3)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.3', 'C.3', 'N.2', 'N.2', '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']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 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]
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, 7, 7, 7, 7, 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, 29, 39, 29, 29, 39, 39, 31, 39, 39, 29, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 39, 39, 33, 39, 39, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29] 39
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 44, 45])
total number of confs: 151
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: REAL300000040580 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=CC3=C2CCCC3)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.3', 'C.3', 'N.2', 'N.2', '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']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 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]
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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [6, 5, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 22, 22, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 1, 1, 1, 1, 1, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5] 39
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 60
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040580 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=CC3=C2CCCC3)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.3', 'C.3', 'N.2', 'N.2', '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']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 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]
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, 7, 7, 7, 7, 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, 1, 3, 1, 1, 5, 5, 1, 5, 5, 1, 1, 1, 11, 11, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 5, 5, 2, 5, 5, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1] 39
rigid atoms, others: [32, 1, 3, 4, 44, 10, 11, 12, 45, 24, 30, 31] set([0, 2, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 58
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040580 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040580
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040580/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040580
Building REAL300000040581
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040581'
/scratch/stefan/7769621/working/building/REAL300000040581 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040581

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040581/0 /scratch/stefan/7769621/working/building/REAL300000040581 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 679)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/679
`/scratch/stefan/7769621/working/3D/679' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC2=C1CCCC2)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C)

`REAL300000040581.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040581.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040581/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040581 none CC(N=NC1=CC=CC2=C1CCCC2)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 5, 5, 7, 5, 1, 11, 11, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 4, 18, 18, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 7, 10, 10, 1, 1, 1, 4, 4, 4, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 7, 7, 2, 2, 2, 2, 2, 2] 48
rigid atoms, others: [1, 41, 42, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 93
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040581 none CC(N=NC1=CC=CC2=C1CCCC2)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 5, 5, 7, 5, 1, 11, 11, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [25, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 31, 31, 31, 31, 31, 48, 48, 48, 31, 31, 31, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 48, 48, 31, 31, 31, 31, 31, 31] 48
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 194
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040581 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040581
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040581/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040581
Building REAL300000040582
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040582'
/scratch/stefan/7769621/working/building/REAL300000040582 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040582

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040582/0 /scratch/stefan/7769621/working/building/REAL300000040582 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 680)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/680
`/scratch/stefan/7769621/working/3D/680' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCCCCCC(=O)[O-])N=NC1=CC=CC2=C1CCCC2)

`REAL300000040582.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040582.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040582/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040582 none CC(CCCCCCC(=O)[O-])N=NC1=CC=CC2=C1CCCC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', '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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 8, 8, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 28, 51, 59, 70, 98, 110, 201, 201, 201, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 55, 55, 56, 59, 75, 75, 94, 98, 116, 116, 198, 196, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 976
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040582 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040582
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040582/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040582
Building REAL300000040583
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040583'
/scratch/stefan/7769621/working/building/REAL300000040583 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040583

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040583/0 /scratch/stefan/7769621/working/building/REAL300000040583 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 681)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/681
`/scratch/stefan/7769621/working/3D/681' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(CC(=O)[O-])CCC1N=NC1=CC=CC2=C1CCCC2)

`REAL300000040583.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040583.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040583/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040583 none CC1C(CC(=O)[O-])CCC1N=NC1=CC=CC2=C1CCCC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 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, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 31, 31, 52, 52, 52, 31, 31, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 29, 31, 52, 52, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 52
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 177
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040583 none CC1C(CC(=O)[O-])CCC1N=NC1=CC=CC2=C1CCCC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 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, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 9, 13, 13, 1, 1, 1, 1, 12, 12, 31, 31, 31, 31, 31, 31, 31, 31, 31, 2, 2, 2, 1, 1, 9, 9, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 52
rigid atoms, others: [0, 1, 2, 3, 32, 33, 7, 8, 9, 10, 25, 26, 29, 30, 31] set([4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 88
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040583 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040583
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040583/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040583
Building REAL300000040584
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040584'
/scratch/stefan/7769621/working/building/REAL300000040584 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040584

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040584/0 /scratch/stefan/7769621/working/building/REAL300000040584 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 682)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/682
`/scratch/stefan/7769621/working/3D/682' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(C)=NNC2=CC=CC3=C2CCCC3)=CC=C1OCCCC(=O)[O-])

`REAL300000040584.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040584.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040584/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040584 none COC1=CC(C(C)=NNC2=CC=CC3=C2CCCC3)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 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]
0  hydrogens 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, 45, 45, 13, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 107, 179, 183, 201, 201, 201, 78, 78, 78, 45, 13, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 179, 179, 183, 183, 201, 201] 201
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 48, 49, 50, 51, 52, 53, 54, 55])
total number of confs: 688
number of broken/clashed sets: 126
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040584 none COC1=CC(C(C)=NNC2=CC=CC3=C2CCCC3)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 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]
0  hydrogens 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, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 7, 17, 19, 29, 45, 45, 3, 3, 3, 1, 7, 7, 7, 21, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 17, 17, 19, 19, 29, 29] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 48, 49, 19, 20, 21, 22] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52, 53, 54, 55])
total number of confs: 282
number of broken/clashed sets: 126
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040584 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040584
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040584/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040584
Building REAL300000040585
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040585'
/scratch/stefan/7769621/working/building/REAL300000040585 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040585

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040585/0 /scratch/stefan/7769621/working/building/REAL300000040585 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 683)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/683
`/scratch/stefan/7769621/working/3D/683' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1(C(=O)[O-])CCC1)N=NC1=CC=CC2=C1CCCC2)

`REAL300000040585.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040585.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040585/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040585 none CC(CC1(C(=O)[O-])CCC1)N=NC1=CC=CC2=C1CCCC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 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, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 6, 27, 46, 66, 66, 66, 66, 66, 66, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 46, 46, 66, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 66
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 249
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040585 none CC(CC1(C(=O)[O-])CCC1)N=NC1=CC=CC2=C1CCCC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 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, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 7, 1, 1, 1, 3, 3, 1, 1, 1, 13, 51, 51, 66, 66, 66, 66, 66, 66, 66, 66, 66, 13, 13, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66] 66
rigid atoms, others: [32, 33, 2, 3, 4, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 138
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040585 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040585
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040585/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040585
Building REAL300000040586
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040586'
/scratch/stefan/7769621/working/building/REAL300000040586 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000040586 as failed and skipping
/scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `/scratch/stefan/7769621/failed'
`/scratch/stefan/7769621/working/building/REAL300000040586' -> `/scratch/stefan/7769621/failed/REAL300000040586'
Building REAL300000040587
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040587'
/scratch/stefan/7769621/working/building/REAL300000040587 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040587

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040587/0 /scratch/stefan/7769621/working/building/REAL300000040587 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 684)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/684
`/scratch/stefan/7769621/working/3D/684' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=CC2=C1CCCC2)

`REAL300000040587.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040587.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040587/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040587 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=CC2=C1CCCC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [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
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [90, 90, 90, 90, 90, 90, 90, 90, 90, 90, 51, 51, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 90, 90, 90, 90, 90, 90, 90, 90, 51, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 90
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 132
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040587 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=CC2=C1CCCC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [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
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 13, 13, 53, 90, 90, 90, 90, 90, 90, 90, 90, 90, 2, 2, 2, 1, 2, 2, 2, 1, 13, 53, 90, 90, 90, 90, 90, 90, 90, 90, 90, 90, 90] 90
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 27, 31] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 206
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040587 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040587
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040587/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040587
Building REAL300000040588
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040588'
/scratch/stefan/7769621/working/building/REAL300000040588 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040588

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040588/0 /scratch/stefan/7769621/working/building/REAL300000040588 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 685)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/685
`/scratch/stefan/7769621/working/3D/685' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(C=NNC2=CC=CC3=C2CCCC3)=C1Cl)

`REAL300000040588.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040588.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040588/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040588 none O=C([O-])C1=CC=CC(C=NNC2=CC=CC3=C2CCCC3)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', '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.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 16, 7, 7, 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, 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]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 37, 37, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 37, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 43
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 68
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040588 none O=C([O-])C1=CC=CC(C=NNC2=CC=CC3=C2CCCC3)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', '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.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 16, 7, 7, 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, 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]
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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 22, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 8, 22, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43] 43
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 85
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040588 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040588
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040588/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040588
Building REAL300000040589
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040589'
/scratch/stefan/7769621/working/building/REAL300000040589 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040589

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040589/0 /scratch/stefan/7769621/working/building/REAL300000040589 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 686)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/686
`/scratch/stefan/7769621/working/3D/686' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=CC3=C2CCCC3)C=C1F)

`REAL300000040589.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040589.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040589/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040589 none O=C([O-])C1=CC=C(C=NNC2=CC=CC3=C2CCCC3)C=C1F NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', '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.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 15, 7, 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, 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]
0  hydrogens need rotated
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [81, 81, 81, 81, 81, 81, 41, 41, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 41, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 81] 81
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 38])
total number of confs: 135
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040589 none O=C([O-])C1=CC=C(C=NNC2=CC=CC3=C2CCCC3)C=C1F NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', '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.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 15, 7, 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, 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]
0  hydrogens need rotated
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 11, 11, 41, 80, 81, 81, 81, 81, 81, 81, 81, 81, 1, 1, 1, 1, 1, 11, 41, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 1] 81
rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 38] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 161
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040589 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040589
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040589/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040589
Building REAL300000040590
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040590'
/scratch/stefan/7769621/working/building/REAL300000040590 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040590

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040590/0 /scratch/stefan/7769621/working/building/REAL300000040590 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 687)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/687
`/scratch/stefan/7769621/working/3D/687' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C=CC1=CC=C(C=NNC2=CC=CC3=C2CCCC3)O1)

`REAL300000040590.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040590.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040590/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040590 none O=C([O-])C=CC1=CC=C(C=NNC2=CC=CC3=C2CCCC3)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [107, 108, 108, 108, 67, 67, 67, 67, 43, 43, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 67, 108, 108, 67, 67, 43, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 108
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 233
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040590 none O=C([O-])C=CC1=CC=C(C=NNC2=CC=CC3=C2CCCC3)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [21, 11, 22, 11, 1, 1, 1, 1, 1, 1, 6, 6, 27, 67, 67, 67, 67, 67, 67, 67, 67, 67, 1, 11, 11, 1, 1, 6, 27, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67] 108
rigid atoms, others: [4, 5, 6, 7, 8, 9, 22, 25, 26] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 173
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040590 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040590
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040590/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040590
Building REAL300000040591
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040591'
/scratch/stefan/7769621/working/building/REAL300000040591 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040591

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040591/0 /scratch/stefan/7769621/working/building/REAL300000040591 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 688)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/688
`/scratch/stefan/7769621/working/3D/688' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2NC=C(C=NNC3=CC=CC4=C3CCCC4)C2=C1)

`REAL300000040591.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040591.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040591/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040591 none O=C([O-])C1=CC=C2NC=C(C=NNC3=CC=CC4=C3CCCC4)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [41, 41, 41, 41, 41, 40, 40, 40, 40, 36, 36, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 41, 41, 40, 40, 40, 36, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41] 41
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 42, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 61
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040591 none O=C([O-])C1=CC=C2NC=C(C=NNC3=CC=CC4=C3CCCC4)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.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: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 23, 41, 41, 41, 41, 41, 40, 40, 41, 41, 1, 1, 1, 1, 1, 1, 5, 22, 41, 41, 41, 40, 40, 40, 40, 41, 41, 41, 41, 1] 41
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 28, 42] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 83
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040591 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040591
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040591/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040591
Building REAL300000040592
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040592'
/scratch/stefan/7769621/working/building/REAL300000040592 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040592

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040592/0 /scratch/stefan/7769621/working/building/REAL300000040592 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 689)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/689
`/scratch/stefan/7769621/working/3D/689' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=CC3=C2CCCC3)C=C1O)

`REAL300000040592.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040592.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040592/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040592 none O=C([O-])C1=CC=C(C=NNC2=CC=CC3=C2CCCC3)C=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', '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.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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 12, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [69, 69, 69, 69, 69, 69, 40, 40, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 40, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69, 138] 138
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 20, 21, 22, 23, 24, 25, 26, 38])
total number of confs: 250
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040592 none O=C([O-])C1=CC=C(C=NNC2=CC=CC3=C2CCCC3)C=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', '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.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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 12, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 10, 10, 41, 69, 69, 68, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 10, 41, 69, 69, 68, 69, 69, 69, 69, 69, 69, 69, 69, 1, 2] 138
rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 38] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39])
total number of confs: 153
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040592 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040592
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040592/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040592
Building REAL300000040593
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040593'
/scratch/stefan/7769621/working/building/REAL300000040593 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040593

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040593/0 /scratch/stefan/7769621/working/building/REAL300000040593 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 690)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/690
`/scratch/stefan/7769621/working/3D/690' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C=NNC2=CC=CC3=C2CCCC3)C=C1C(=O)[O-])

`REAL300000040593.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040593.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040593/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040593 none CC1=CC=C(C=NNC2=CC=CC3=C2CCCC3)C=C1C(=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.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']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 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]
dock color type numbers: [7, 7, 7, 7, 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]
0  hydrogens need rotated
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 67, 44, 44, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 44, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 67] 67
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 41, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 103
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040593 none CC1=CC=C(C=NNC2=CC=CC3=C2CCCC3)C=C1C(=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.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']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 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]
dock color type numbers: [7, 7, 7, 7, 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]
0  hydrogens need rotated
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 37, 67, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 7, 36, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 1] 67
rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 18, 19, 20, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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
/scratch/stefan/7769621/working/building/REAL300000040593 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040593
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040593/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040593
Building REAL300000040594
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040594'
/scratch/stefan/7769621/working/building/REAL300000040594 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040594

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040594/0 /scratch/stefan/7769621/working/building/REAL300000040594 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 691)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/691
`/scratch/stefan/7769621/working/3D/691' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Cl)SC(C=NNC2=CC=CC3=C2CCCC3)=C1)

`REAL300000040594.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040594.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040594/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040594 none O=C([O-])C1=C(Cl)SC(C=NNC2=CC=CC3=C2CCCC3)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 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, 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]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [113, 113, 113, 113, 113, 113, 113, 53, 53, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 113, 53, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 113] 113
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 21, 22, 23])
total number of confs: 169
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040594 none O=C([O-])C1=C(Cl)SC(C=NNC2=CC=CC3=C2CCCC3)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 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, 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]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 51, 113, 113, 113, 113, 113, 113, 113, 113, 113, 1, 8, 51, 113, 113, 113, 113, 113, 113, 113, 113, 113, 113, 113, 1] 113
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 35, 21] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 207
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040594 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040594
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040594/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040594
Building REAL300000040595
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040595'
/scratch/stefan/7769621/working/building/REAL300000040595 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040595

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040595/0 /scratch/stefan/7769621/working/building/REAL300000040595 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 692)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/692
`/scratch/stefan/7769621/working/3D/692' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=CC4=C3CCCC4)O2)=CC=C1O)

`REAL300000040595.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040595.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040595/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040595 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=CC4=C3CCCC4)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 87, 87, 87, 87, 44, 44, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 87, 201, 201, 201, 201, 201, 87, 87, 44, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 402] 402
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 44, 45, 46])
total number of confs: 686
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: REAL300000040595 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=CC4=C3CCCC4)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [25, 13, 25, 12, 12, 1, 1, 1, 1, 1, 1, 7, 7, 36, 87, 87, 87, 87, 87, 87, 87, 87, 87, 1, 12, 12, 12, 12, 12, 1, 1, 7, 36, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 12, 12, 24] 402
rigid atoms, others: [5, 6, 7, 8, 9, 10, 23, 29, 30] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 243
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040595 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=CC4=C3CCCC4)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 12, 12, 12, 12, 44, 44, 138, 201, 201, 201, 201, 201, 201, 201, 201, 201, 12, 1, 1, 1, 1, 1, 12, 12, 44, 138, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 2] 402
rigid atoms, others: [1, 3, 4, 5, 6, 44, 45, 24, 25, 26, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46])
total number of confs: 450
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040595 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040595
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040595/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040595
Building REAL300000040596
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040596'
/scratch/stefan/7769621/working/building/REAL300000040596 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040596

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040596/0 /scratch/stefan/7769621/working/building/REAL300000040596 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 693)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/693
`/scratch/stefan/7769621/working/3D/693' -> `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=NNC1=CC=CC2=C1CCCC2)

`REAL300000040596.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040596.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040596/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040596 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC2=C1CCCC2 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.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, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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]
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, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 22, 22, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 22, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 28
rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 49
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040596 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC2=C1CCCC2 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.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, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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]
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, 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: [3, 1, 3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 4, 4, 13, 28, 28, 28, 28, 28, 28, 28, 28, 28, 3, 3, 3, 3, 3, 3, 1, 1, 1, 4, 13, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 28
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 10, 11, 12, 33, 31] set([0, 2, 8, 9, 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, 45, 46])
total number of confs: 64
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040596 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040596
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040596/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040596
Building REAL300000040597
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040597'
/scratch/stefan/7769621/working/building/REAL300000040597 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040597

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040597/0 /scratch/stefan/7769621/working/building/REAL300000040597 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 694)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/694
`/scratch/stefan/7769621/working/3D/694' -> `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=NNC3=CC=CC4=C3CCCC4)S2)=C1)

`REAL300000040597.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040597.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040597/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040597 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=CC4=C3CCCC4)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 1, 7, 7, 7, 7, 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, 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, 7]
0  hydrogens need rotated
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, 93, 93, 93, 93, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 93, 201, 201, 201, 201, 93, 93, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201
rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 45])
total number of confs: 298
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: REAL300000040597 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=CC4=C3CCCC4)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 1, 7, 7, 7, 7, 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, 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, 7]
0  hydrogens 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, 6, 6, 38, 93, 93, 92, 93, 93, 93, 93, 93, 93, 1, 12, 12, 12, 12, 1, 1, 6, 38, 93, 93, 92, 93, 93, 93, 93, 93, 93, 93, 93, 12] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 25, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 179
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040597 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=CC4=C3CCCC4)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 1, 7, 7, 7, 7, 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, 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, 7]
0  hydrogens need rotated
201  conformations 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, 54, 54, 146, 201, 201, 201, 201, 201, 201, 201, 201, 201, 12, 1, 1, 1, 1, 12, 12, 54, 146, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 45, 26, 27, 28, 29] set([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: 451
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040597 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040597
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040597/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040597
Building REAL300000040598
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040598'
/scratch/stefan/7769621/working/building/REAL300000040598 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040598

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040598/0 /scratch/stefan/7769621/working/building/REAL300000040598 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 695)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/695
`/scratch/stefan/7769621/working/3D/695' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC2=C1CCCC2)

`REAL300000040598.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040598.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040598/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040598 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC2=C1CCCC2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 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]
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: [141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 48, 48, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 142, 142, 142, 141, 141, 141, 48, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 142
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 203
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040598 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC2=C1CCCC2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 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]
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, 1, 1, 1, 1, 12, 12, 67, 141, 141, 141, 141, 141, 141, 141, 141, 141, 4, 4, 4, 1, 1, 1, 12, 67, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141] 142
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 273
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040598 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040598
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040598/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040598
Building REAL300000040599
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040599'
/scratch/stefan/7769621/working/building/REAL300000040599 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040599

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040599/0 /scratch/stefan/7769621/working/building/REAL300000040599 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 696)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/696
`/scratch/stefan/7769621/working/3D/696' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=CC4=C3CCCC4)C2=C1)

`REAL300000040599.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040599.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040599/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040599 none O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=CC4=C3CCCC4)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 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, 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]
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, 44, 44, 44, 44, 44, 44, 44, 44, 35, 35, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 35, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44] 44
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 41, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 68
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040599 none O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=CC4=C3CCCC4)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 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, 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]
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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 25, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 1, 6, 25, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1] 44
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 41, 23, 24, 25, 26, 27] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 90
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040599 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040599
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040599/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040599
Building REAL300000040600
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040600'
/scratch/stefan/7769621/working/building/REAL300000040600 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040600

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040600/0 /scratch/stefan/7769621/working/building/REAL300000040600 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 697)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/697
`/scratch/stefan/7769621/working/3D/697' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=CC3=C2CCCC3)=C1)

`REAL300000040600.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040600.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040600/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040600 none O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=CC3=C2CCCC3)=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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 7, 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, 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]
0  hydrogens need rotated
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [82, 82, 82, 82, 82, 82, 82, 82, 45, 45, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 45, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 82] 82
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 38])
total number of confs: 123
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040600 none O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=CC3=C2CCCC3)=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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 7, 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, 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]
0  hydrogens need rotated
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 43, 82, 82, 82, 82, 82, 82, 82, 82, 82, 1, 1, 1, 12, 43, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 1] 82
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 38] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/7769621/working/building/REAL300000040600 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040600
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040600/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040600
Building REAL300000040601
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040601'
/scratch/stefan/7769621/working/building/REAL300000040601 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040601

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040601/0 /scratch/stefan/7769621/working/building/REAL300000040601 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 698)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/698
`/scratch/stefan/7769621/working/3D/698' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=CC=CC3=C2CCCC3)=CC=C1C(=O)[O-])

`REAL300000040601.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040601.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040601/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040601 none COC1=CC(C=NNC2=CC=CC3=C2CCCC3)=CC=C1C(=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.ar', 'C.ar', 'C.3', 'C.3', 'C.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, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 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
173  conformations in input
total number of sets (complete confs): 173
using faster count positions algorithm for large data
unique positions, atoms: [173, 136, 136, 136, 56, 56, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 136, 136, 136, 136, 173, 173, 173, 173, 173, 136, 56, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 136, 136] 173
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 41, 42, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 423
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040601 none COC1=CC(C=NNC2=CC=CC3=C2CCCC3)=CC=C1C(=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.ar', 'C.ar', 'C.3', 'C.3', 'C.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, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 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
173  conformations in input
total number of sets (complete confs): 173
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 10, 10, 52, 136, 136, 136, 136, 136, 136, 136, 136, 136, 1, 1, 1, 1, 3, 3, 4, 4, 4, 1, 10, 51, 136, 136, 136, 136, 136, 136, 136, 136, 136, 136, 136, 1, 1] 173
rigid atoms, others: [1, 2, 3, 4, 5, 41, 42, 18, 19, 20, 21, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 240
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040601 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040601
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040601/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040601
Building REAL300000040602
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040602'
/scratch/stefan/7769621/working/building/REAL300000040602 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040602

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040602/0 /scratch/stefan/7769621/working/building/REAL300000040602 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 699)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/699
`/scratch/stefan/7769621/working/3D/699' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(F)=C(C=NNC2=CC=CC3=C2CCCC3)C(F)=C1)

`REAL300000040602.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040602.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040602/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040602 none O=C([O-])C1=CC(F)=C(C=NNC2=CC=CC3=C2CCCC3)C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.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, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 15, 1, 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, 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]
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: [39, 39, 40, 33, 40, 40, 40, 30, 30, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 30, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40] 40
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 38])
total number of confs: 99
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040602 none O=C([O-])C1=CC(F)=C(C=NNC2=CC=CC3=C2CCCC3)C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.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, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 15, 1, 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, 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]
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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 29, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 7, 29, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1] 40
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 38] set([0, 2, 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: 95
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040602 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040602
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040602/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040602
Building REAL300000040603
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040603'
/scratch/stefan/7769621/working/building/REAL300000040603 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040603

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040603/0 /scratch/stefan/7769621/working/building/REAL300000040603 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 700)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/700
`/scratch/stefan/7769621/working/3D/700' -> `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=NNC2=CC=CC3=C2CCCC3)=C1)

`REAL300000040603.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040603.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040603/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040603 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=CC=CC3=C2CCCC3)=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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 7, 6, 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, 7, 4, 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]
1  hydrogens need rotated
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [74, 74, 74, 74, 74, 74, 74, 74, 74, 43, 43, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 74, 74, 148, 43, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 74] 148
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 39])
total number of confs: 258
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040603 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=CC=CC3=C2CCCC3)=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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 7, 6, 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, 7, 4, 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]
1  hydrogens need rotated
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 45, 74, 74, 74, 74, 74, 74, 74, 74, 74, 1, 1, 2, 12, 45, 74, 74, 74, 74, 74, 74, 74, 74, 74, 74, 74, 1] 148
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 23, 24] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 159
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040603 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040603/1 /scratch/stefan/7769621/working/building/REAL300000040603 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 701)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/701
`/scratch/stefan/7769621/working/3D/701' -> `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=NNC2=CC=CC3=C2CCCC3)=C1)

`REAL300000040603.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040603.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040603/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040603 none O=C([O-])C1=CC(Br)=C([O-])C(C=NNC2=CC=CC3=C2CCCC3)=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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 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, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 25, 25, 23, 23, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 23, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25] 25
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 38])
total number of confs: 46
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040603 none O=C([O-])C1=CC(Br)=C([O-])C(C=NNC2=CC=CC3=C2CCCC3)=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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 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, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 4, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1] 25
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 38] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 49
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040603 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040603
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040603/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040603/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040603
Building REAL300000040604
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040604'
/scratch/stefan/7769621/working/building/REAL300000040604 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040604

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040604/0 /scratch/stefan/7769621/working/building/REAL300000040604 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 702)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/702
`/scratch/stefan/7769621/working/3D/702' -> `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=NNC3=CC=CC4=C3CCCC4)C=C2)O1)

`REAL300000040604.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040604.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040604/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040604 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=CC=CC4=C3CCCC4)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 12, 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: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 136, 104, 62, 38, 104, 103, 37, 37, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 104, 104, 201, 201, 201, 136, 136, 104, 103, 37, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 104, 104] 201
rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 48, 49])
total number of confs: 653
number of broken/clashed sets: 45
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040604 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=CC=CC4=C3CCCC4)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 12, 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: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 26, 27, 26, 26, 26, 7, 1, 1, 1, 1, 1, 1, 1, 10, 10, 44, 103, 103, 103, 103, 103, 103, 104, 104, 103, 1, 1, 26, 26, 27, 7, 7, 1, 1, 10, 44, 103, 103, 103, 103, 103, 104, 104, 104, 104, 103, 103, 1, 1] 201
rigid atoms, others: [33, 34, 7, 8, 9, 10, 11, 12, 13, 48, 49, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 231
number of broken/clashed sets: 45
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040604 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=CC=CC4=C3CCCC4)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 12, 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: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 1, 1, 1, 1, 1, 8, 26, 26, 26, 26, 26, 74, 74, 121, 201, 201, 201, 201, 201, 201, 201, 201, 201, 26, 26, 1, 1, 1, 8, 8, 27, 27, 74, 121, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 26, 26] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 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, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 443
number of broken/clashed sets: 45
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040604 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040604
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040604/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040604
Building REAL300000040605
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040605'
/scratch/stefan/7769621/working/building/REAL300000040605 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040605

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040605/0 /scratch/stefan/7769621/working/building/REAL300000040605 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 703)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/703
`/scratch/stefan/7769621/working/3D/703' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=CC3=C2CCCC3)=C1O)

`REAL300000040605.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040605.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040605/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040605 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=CC3=C2CCCC3)=C1O 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.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 41, 41, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 69, 69, 41, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 138] 138
rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 45])
total number of confs: 244
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040605 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=CC3=C2CCCC3)=C1O 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.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 32, 69, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 1, 10, 32, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 2] 138
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 137
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040605 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040605
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040605/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040605
Building REAL300000040606
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040606'
/scratch/stefan/7769621/working/building/REAL300000040606 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040606

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040606/0 /scratch/stefan/7769621/working/building/REAL300000040606 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 704)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/704
`/scratch/stefan/7769621/working/3D/704' -> `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=NNC3=CC=CC4=C3CCCC4)C=C2)=C1)

`REAL300000040606.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040606.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040606/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040606 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=CC4=C3CCCC4)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [2, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 130, 130, 130, 130, 130, 72, 72, 93, 93, 40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 93, 93, 130, 201, 201, 130, 130, 130, 93, 93, 40, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 93, 93, 130] 201
rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 49, 50, 51])
total number of confs: 720
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: REAL300000040606 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=CC4=C3CCCC4)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [2, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 5, 13, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 42, 93, 93, 93, 93, 93, 93, 93, 93, 93, 1, 1, 3, 5, 5, 3, 3, 3, 1, 1, 10, 42, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 1, 1, 3] 201
rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 49, 50, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 51])
total number of confs: 211
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040606 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=CC4=C3CCCC4)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [2, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 12, 12, 57, 128, 128, 125, 128, 128, 128, 128, 129, 128, 3, 3, 1, 2, 2, 1, 1, 1, 3, 3, 12, 57, 128, 128, 127, 128, 128, 128, 128, 128, 128, 128, 128, 3, 3, 1] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 51, 28, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 279
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040606 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040606
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040606/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040606
Building REAL300000040607
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040607'
/scratch/stefan/7769621/working/building/REAL300000040607 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040607

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040607/0 /scratch/stefan/7769621/working/building/REAL300000040607 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 705)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/705
`/scratch/stefan/7769621/working/3D/705' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C=NNC2=CC=CC3=C2CCCC3)=CS1)

`REAL300000040607.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040607.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040607/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040607 none O=C([O-])C1=CC(C=NNC2=CC=CC3=C2CCCC3)=CS1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', '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, 5, 5, 5, 5, 1, 14, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [47, 47, 47, 47, 47, 36, 36, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 36, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47] 47
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 35])
total number of confs: 75
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040607 none O=C([O-])C1=CC(C=NNC2=CC=CC3=C2CCCC3)=CS1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', '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, 5, 5, 5, 5, 1, 14, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 8, 8, 31, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 8, 31, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1] 47
rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 35] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 103
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040607 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040607
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040607/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040607
Building REAL300000040608
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040608'
/scratch/stefan/7769621/working/building/REAL300000040608 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040608

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040608/0 /scratch/stefan/7769621/working/building/REAL300000040608 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 706)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/706
`/scratch/stefan/7769621/working/3D/706' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC(C=NNC2=CC=CC3=C2CCCC3)=CC=C1OCC(=O)[O-])

`REAL300000040608.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040608.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040608/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040608 none CCOC1=CC(C=NNC2=CC=CC3=C2CCCC3)=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.ar', 'C.ar', '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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [7, 7, 3, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [97, 68, 25, 25, 25, 10, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 110, 185, 191, 191, 97, 97, 97, 97, 97, 25, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 185, 185] 201
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 46, 47, 48, 49])
total number of confs: 764
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040608 none CCOC1=CC(C=NNC2=CC=CC3=C2CCCC3)=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.ar', 'C.ar', '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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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]
dock color type numbers: [7, 7, 3, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 7, 1, 1, 1, 1, 1, 7, 7, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 9, 37, 68, 68, 20, 20, 20, 20, 20, 1, 7, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 37, 37] 201
rigid atoms, others: [32, 2, 3, 4, 5, 6, 46, 47, 19, 20, 21, 22] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49])
total number of confs: 337
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040608 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040608
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040608/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040608
Building REAL300000040609
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040609'
/scratch/stefan/7769621/working/building/REAL300000040609 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040609

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040609/0 /scratch/stefan/7769621/working/building/REAL300000040609 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 707)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/707
`/scratch/stefan/7769621/working/3D/707' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCC1=CC=C(C=NNC2=CC=CC3=C2CCCC3)O1)

`REAL300000040609.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040609.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040609/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040609 none O=C([O-])CCC1=CC=C(C=NNC2=CC=CC3=C2CCCC3)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 194, 175, 73, 73, 73, 73, 43, 43, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 73, 201, 201, 175, 175, 73, 73, 43, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 730
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040609 none O=C([O-])CCC1=CC=C(C=NNC2=CC=CC3=C2CCCC3)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 19, 23, 9, 1, 1, 1, 1, 1, 1, 6, 6, 29, 73, 73, 73, 73, 73, 73, 73, 73, 73, 1, 19, 19, 9, 9, 1, 1, 6, 29, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 22, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 246
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040609 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040609
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040609/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040609
Building REAL300000040610
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040610'
/scratch/stefan/7769621/working/building/REAL300000040610 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040610

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040610/0 /scratch/stefan/7769621/working/building/REAL300000040610 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 708)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/708
`/scratch/stefan/7769621/working/3D/708' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C2NC=C(C=NNC3=CC=CC4=C3CCCC4)C2=CC=C1)

`REAL300000040610.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040610.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040610/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040610 none O=C([O-])C1=C2NC=C(C=NNC3=CC=CC4=C3CCCC4)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 6, 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, 4, 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]
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, 66, 67, 66, 66, 66, 66, 43, 43, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 67, 67, 67, 66, 66, 43, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67] 67
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 41, 40, 21, 22, 23, 24, 25, 26, 27, 28, 42])
total number of confs: 110
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040610 none O=C([O-])C1=C2NC=C(C=NNC3=CC=CC4=C3CCCC4)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 6, 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, 4, 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]
0  hydrogens need rotated
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 37, 67, 67, 67, 67, 67, 66, 66, 67, 67, 1, 1, 1, 1, 1, 1, 7, 36, 67, 67, 67, 66, 66, 66, 66, 67, 67, 67, 67, 1, 1, 1] 67
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 41, 42, 40, 21, 22, 23, 24, 25, 26] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 136
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040610 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040610
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040610/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040610
Building REAL300000040611
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040611'
/scratch/stefan/7769621/working/building/REAL300000040611 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040611

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040611/0 /scratch/stefan/7769621/working/building/REAL300000040611 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 709)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/709
`/scratch/stefan/7769621/working/3D/709' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC(C=NNC3=CC=CC4=C3CCCC4)=CC=C2O1)

`REAL300000040611.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040611.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040611/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040611 none O=C([O-])C1=CC2=CC(C=NNC3=CC=CC4=C3CCCC4)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', '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.3', 'C.3', 'C.3', 'C.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', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 12, 7, 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, 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, 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, 70, 42, 42, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 70, 70, 42, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 70, 70] 70
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 41, 40, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 117
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040611 none O=C([O-])C1=CC2=CC(C=NNC3=CC=CC4=C3CCCC4)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', '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.3', 'C.3', 'C.3', 'C.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', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 12, 7, 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, 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, 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, 1, 9, 9, 29, 70, 70, 70, 70, 70, 70, 70, 70, 70, 1, 1, 1, 1, 1, 1, 9, 29, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 1, 1] 70
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 41, 40, 21, 22, 23, 24, 25, 26] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 129
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040611 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040611
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040611/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040611
Building REAL300000040612
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040612'
/scratch/stefan/7769621/working/building/REAL300000040612 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040612

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040612/0 /scratch/stefan/7769621/working/building/REAL300000040612 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 710)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/710
`/scratch/stefan/7769621/working/3D/710' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2C(C=NNC3=CC=CC4=C3CCCC4)=CC=CN12)

`REAL300000040612.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040612.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040612/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040612 none O=C([O-])C1=CN=C2C(C=NNC3=CC=CC4=C3CCCC4)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', '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', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 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, 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
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, 33, 33, 34, 34, 33, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 33, 33, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34] 34
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 41, 39, 40, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 55
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040612 none O=C([O-])C1=CN=C2C(C=NNC3=CC=CC4=C3CCCC4)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', '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', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 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, 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
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 19, 33, 33, 33, 33, 33, 34, 34, 34, 34, 1, 1, 1, 1, 1, 4, 19, 33, 34, 33, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1] 34
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 39, 40, 21, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 71
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040612 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040612
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040612/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040612
Building REAL300000040613
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040613'
/scratch/stefan/7769621/working/building/REAL300000040613 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040613

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040613/0 /scratch/stefan/7769621/working/building/REAL300000040613 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 711)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/711
`/scratch/stefan/7769621/working/3D/711' -> `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=NNC2=CC=CC3=C2CCCC3)O1)

`REAL300000040613.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040613.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040613/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040613 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=CC3=C2CCCC3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 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: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 151, 62, 19, 19, 19, 19, 19, 19, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 151, 151, 19, 19, 19, 19, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 568
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: REAL300000040613 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=CC3=C2CCCC3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 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: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [115, 115, 115, 115, 115, 115, 32, 7, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 115, 115, 115, 32, 32, 1, 1, 1, 1, 4, 8, 19, 19, 19, 19, 19, 19, 19, 19, 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, 45, 46, 47, 48, 49])
total number of confs: 249
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040613 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=CC3=C2CCCC3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 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: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 1, 1, 1, 1, 1, 8, 42, 115, 115, 115, 115, 115, 115, 140, 140, 176, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 8, 8, 115, 115, 115, 115, 140, 176, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 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, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 462
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040613 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040613
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040613/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040613
Building REAL300000040614
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040614'
/scratch/stefan/7769621/working/building/REAL300000040614 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040614

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040614/0 /scratch/stefan/7769621/working/building/REAL300000040614 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 712)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/712
`/scratch/stefan/7769621/working/3D/712' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=CC3=C2CCCC3)C=C1Cl)

`REAL300000040614.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040614.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040614/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040614 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC3=C2CCCC3)C=C1Cl 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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 65, 40, 66, 66, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 201, 201, 66, 66, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 42, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 567
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040614 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC3=C2CCCC3)C=C1Cl 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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 36, 66, 8, 1, 1, 1, 1, 1, 1, 7, 7, 30, 65, 66, 66, 66, 66, 66, 66, 66, 66, 1, 1, 1, 36, 36, 1, 1, 7, 30, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 42, 22, 23, 24, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 345
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040614 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040614
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040614/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040614
Building REAL300000040615
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040615'
/scratch/stefan/7769621/working/building/REAL300000040615 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040615

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040615/0 /scratch/stefan/7769621/working/building/REAL300000040615 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 713)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/713
`/scratch/stefan/7769621/working/3D/713' -> `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=NNC2=CC=CC3=C2CCCC3)C=C1)

`REAL300000040615.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040615.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040615/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040615 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC2=CC=CC3=C2CCCC3)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', 'N.pl3', 'C.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: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 6, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 56, 56, 51, 32, 11, 32, 32, 10, 32, 31, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 56, 56, 51, 32, 31, 10, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32] 56
rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 45, 46])
total number of confs: 277
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040615 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC2=CC=CC3=C2CCCC3)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', 'N.pl3', 'C.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: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 6, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 14, 31, 31, 31, 31, 31, 31, 32, 32, 31, 1, 1, 9, 9, 5, 1, 1, 6, 14, 31, 31, 31, 31, 31, 32, 32, 32, 32, 31, 31, 1, 1] 56
rigid atoms, others: [5, 8, 9, 10, 11, 12, 45, 46, 25, 26, 30, 31] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 107
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040615 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040615
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040615/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040615
Building REAL300000040616
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040616'
/scratch/stefan/7769621/working/building/REAL300000040616 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040616

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040616/0 /scratch/stefan/7769621/working/building/REAL300000040616 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 714)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/714
`/scratch/stefan/7769621/working/3D/714' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=C(C=NNC3=CC=CC4=C3CCCC4)C(F)=CC=C2S1)

`REAL300000040616.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040616.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040616/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040616 none O=C([O-])C1=CC2=C(C=NNC3=CC=CC4=C3CCCC4)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 15, 1, 1, 1, 14, 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, 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]
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, 69, 70, 69, 69, 69, 37, 37, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 69, 69, 37, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69] 70
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 40, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 110
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040616 none O=C([O-])C1=CC2=C(C=NNC3=CC=CC4=C3CCCC4)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 15, 1, 1, 1, 14, 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, 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]
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, 11, 40, 69, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 1, 11, 40, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1] 70
rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 41, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 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: 148
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040616 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040616
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040616/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040616
Building REAL300000040617
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040617'
/scratch/stefan/7769621/working/building/REAL300000040617 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040617

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040617/0 /scratch/stefan/7769621/working/building/REAL300000040617 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 715)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/715
`/scratch/stefan/7769621/working/3D/715' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=CC2=C1CCCC2)

`REAL300000040617.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040617.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040617/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040617 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=CC2=C1CCCC2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 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]
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, 53, 53, 53, 53, 34, 34, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 34, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 53
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 85
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040617 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=CC2=C1CCCC2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 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]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 28, 53, 53, 53, 53, 53, 53, 53, 53, 53, 4, 4, 4, 1, 1, 1, 8, 28, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53] 53
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 111
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040617 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040617
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040617/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040617
Building REAL300000040618
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040618'
/scratch/stefan/7769621/working/building/REAL300000040618 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040618

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040618/0 /scratch/stefan/7769621/working/building/REAL300000040618 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 716)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/716
`/scratch/stefan/7769621/working/3D/716' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=CC4=C3CCCC4)=N2)C1)

`REAL300000040618.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040618.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040618/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040618 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=CC4=C3CCCC4)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 5, 7, 7, 7, 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, 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, 7]
0  hydrogens need rotated
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, 76, 201, 76, 76, 76, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 76, 201, 201, 201, 76, 75, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 44, 45])
total number of confs: 464
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040618 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=CC4=C3CCCC4)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 5, 7, 7, 7, 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, 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, 7]
0  hydrogens 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, 13, 25, 13, 13, 13, 1, 13, 1, 1, 1, 1, 1, 4, 4, 25, 75, 75, 75, 75, 75, 75, 76, 76, 75, 1, 13, 13, 13, 1, 1, 4, 25, 75, 75, 75, 76, 75, 76, 76, 76, 76, 76, 75, 13, 13] 201
rigid atoms, others: [6, 8, 9, 10, 11, 12, 25, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 203
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040618 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=CC4=C3CCCC4)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 5, 7, 7, 7, 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, 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, 7]
0  hydrogens 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, 13, 13, 13, 13, 35, 35, 122, 201, 201, 201, 201, 201, 201, 201, 201, 201, 13, 1, 1, 1, 13, 13, 35, 122, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 44, 45, 26, 27, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 419
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040618 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040618
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040618/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040618
Building REAL300000040619
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040619'
/scratch/stefan/7769621/working/building/REAL300000040619 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040619

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040619/0 /scratch/stefan/7769621/working/building/REAL300000040619 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 717)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/717
`/scratch/stefan/7769621/working/3D/717' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=CC=C1C=NNC(=O)CC(F)(F)F)

`REAL300000040619.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040619.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040619/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040619 none O=C([O-])COC1=CC=CC=C1C=NNC(=O)CC(F)(F)F 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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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, 11, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 47, 78, 9, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 67, 67, 67, 67, 47, 47, 1, 1, 1, 1, 4, 10, 67, 67] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30])
total number of confs: 478
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040619 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040619
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040619/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040619
Building REAL300000040620
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040620'
/scratch/stefan/7769621/working/building/REAL300000040620 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040620

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040620/0 /scratch/stefan/7769621/working/building/REAL300000040620 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 718)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/718
`/scratch/stefan/7769621/working/3D/718' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)CC(F)(F)F)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1)

`REAL300000040620.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040620.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040620/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040620 none CC(=NNC(=O)CC(F)(F)F)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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 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]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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]
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: [13, 1, 13, 13, 71, 73, 78, 129, 129, 129, 129, 1, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 61, 129, 129, 13, 13, 1, 1, 13, 13] 129
rigid atoms, others: [34, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 437
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040620 none CC(=NNC(=O)CC(F)(F)F)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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 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]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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]
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: [6, 1, 6, 6, 31, 31, 31, 91, 91, 91, 91, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 1, 1, 6, 6, 6, 31, 91, 91, 1, 1, 13, 13, 1, 1] 129
rigid atoms, others: [32, 1, 35, 36, 11, 12, 13, 14, 15, 23, 24, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34])
total number of confs: 320
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040620 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040620
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040620/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040620
Building REAL300000040621
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040621'
/scratch/stefan/7769621/working/building/REAL300000040621 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040621

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040621/0 /scratch/stefan/7769621/working/building/REAL300000040621 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 719)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/719
`/scratch/stefan/7769621/working/3D/719' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)CC(F)(F)F)=CC=C1OCC(=O)[O-])

`REAL300000040621.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040621.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040621/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040621 none COC1=CC(C=NNC(=O)CC(F)(F)F)=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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 12, 5, 1, 11, 11, 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, 6, 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]
0  hydrogens 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, 7, 7, 37, 37, 37, 37, 1, 1, 1, 1, 9, 35, 56, 56, 3, 3, 3, 1, 7, 7, 37, 37, 1, 1, 35, 35] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 15, 16, 17, 18, 26, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 33, 34])
total number of confs: 309
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040621 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040621
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040621/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040621
Building REAL300000040622
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040622'
/scratch/stefan/7769621/working/building/REAL300000040622 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040622

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040622/0 /scratch/stefan/7769621/working/building/REAL300000040622 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 720)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/720
`/scratch/stefan/7769621/working/3D/720' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC(=O)CC(F)(F)F)C=C1)

`REAL300000040622.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040622.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040622/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040622 none O=C([O-])COC1=CC=C(C=NNC(=O)CC(F)(F)F)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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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, 11, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 28, 4, 1, 1, 1, 1, 1, 1, 10, 10, 20, 20, 20, 84, 84, 84, 84, 1, 1, 18, 18, 1, 1, 10, 20, 84, 84, 1, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 19, 20, 23, 24, 29, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 25, 26, 27, 28])
total number of confs: 385
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040622 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040622
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040622/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040622
Building REAL300000040623
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040623'
/scratch/stefan/7769621/working/building/REAL300000040623 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040623

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040623/0 /scratch/stefan/7769621/working/building/REAL300000040623 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 721)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/721
`/scratch/stefan/7769621/working/3D/721' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)CC(F)(F)F)C1=CC=CC(OCC(=O)[O-])=C1)

`REAL300000040623.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040623.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040623/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040623 none CC(=NNC(=O)CC(F)(F)F)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 1, 11, 11, 16, 16, 16, 58, 58, 58, 58, 1, 1, 1, 1, 1, 1, 6, 20, 32, 32, 1, 11, 11, 11, 16, 58, 58, 1, 1, 1, 20, 20, 1] 201
rigid atoms, others: [1, 33, 11, 12, 13, 14, 15, 16, 21, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 31, 32])
total number of confs: 301
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040623 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040623
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040623/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040623
Building REAL300000040624
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040624'
/scratch/stefan/7769621/working/building/REAL300000040624 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040624

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040624/0 /scratch/stefan/7769621/working/building/REAL300000040624 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 722)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/722
`/scratch/stefan/7769621/working/3D/722' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)CC(F)(F)F)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1)

`REAL300000040624.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040624.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040624/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040624 none CC(=NNC(=O)CC(F)(F)F)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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]
0  hydrogens need rotated
135  conformations in input
total number of sets (complete confs): 135
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 10, 10, 10, 52, 52, 52, 52, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 17, 1, 1, 6, 6, 6, 10, 52, 52, 1, 1, 9, 17, 17, 1, 1] 135
rigid atoms, others: [32, 1, 36, 37, 11, 12, 13, 14, 15, 23, 24, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35])
total number of confs: 255
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040624 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040624
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040624/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040624
Building REAL300000040625
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040625'
/scratch/stefan/7769621/working/building/REAL300000040625 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040625

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040625/0 /scratch/stefan/7769621/working/building/REAL300000040625 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 723)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/723
`/scratch/stefan/7769621/working/3D/723' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)CC(F)(F)F)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1)

`REAL300000040625.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040625.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040625/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040625 none CC(=NNC(=O)CC(F)(F)F)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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]
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: [5, 1, 5, 5, 8, 8, 8, 18, 18, 18, 18, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 1, 1, 5, 5, 5, 8, 18, 18, 1, 1, 9, 9, 9, 9, 9, 1, 1] 80
rigid atoms, others: [32, 1, 33, 40, 11, 12, 13, 14, 15, 24, 25, 39] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38])
total number of confs: 90
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040625 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040625
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040625/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040625
Building REAL300000040626
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040626'
/scratch/stefan/7769621/working/building/REAL300000040626 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040626

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040626/0 /scratch/stefan/7769621/working/building/REAL300000040626 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 724)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/724
`/scratch/stefan/7769621/working/3D/724' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)CC(F)(F)F)C1=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C1)

`REAL300000040626.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040626.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040626/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040626 none CC(=NNC(=O)CC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 1, 14, 11, 11, 8, 5, 7, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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
7  conformations in input
total number of sets (complete confs): 7
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 3, 3, 3, 3, 5, 5, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 1, 1, 3, 3, 3, 3, 5, 5, 1, 1, 4, 4, 4, 4, 1, 1] 7
rigid atoms, others: [1, 34, 33, 40, 11, 12, 13, 14, 15, 25, 26, 39] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38])
total number of confs: 31
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040626 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040626
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040626/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040626
Building REAL300000040627
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040627'
/scratch/stefan/7769621/working/building/REAL300000040627 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040627

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040627/0 /scratch/stefan/7769621/working/building/REAL300000040627 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 725)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/725
`/scratch/stefan/7769621/working/3D/725' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)CC(F)(F)F)C1=CC=C(CC(=O)[O-])C=C1)

`REAL300000040627.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040627.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040627/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040627 none CC(=NNC(=O)CC(F)(F)F)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [6, 1, 6, 6, 18, 18, 18, 48, 48, 48, 48, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 6, 6, 6, 18, 48, 48, 1, 1, 3, 3, 1, 1] 69
rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 19, 20, 27, 28, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29, 30])
total number of confs: 194
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040627 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040627
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040627/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040627
Building REAL300000040628
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040628'
/scratch/stefan/7769621/working/building/REAL300000040628 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040628

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040628/0 /scratch/stefan/7769621/working/building/REAL300000040628 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 726)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/726
`/scratch/stefan/7769621/working/3D/726' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])OC2=C1C(=NNC(=O)CC(F)(F)F)CCC2)

`REAL300000040628.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040628.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040628/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040628 none CC1=C(C(=O)[O-])OC2=C1C(=NNC(=O)CC(F)(F)F)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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', '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, 1, 11, 5, 5, 15, 15, 15, 5, 5, 5, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 32, 32, 32, 32, 1, 1, 1, 2, 2, 2, 7, 32, 32, 1, 1, 1, 1, 1, 1] 33
rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 28, 29, 30, 31] set([4, 5, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27])
total number of confs: 118
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040628 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040628
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040628/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040628
Building REAL300000040629
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040629'
/scratch/stefan/7769621/working/building/REAL300000040629 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040629

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040629/0 /scratch/stefan/7769621/working/building/REAL300000040629 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 727)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/727
`/scratch/stefan/7769621/working/3D/727' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=C(C=NNC(=O)CC(F)(F)F)C=C1)

`REAL300000040629.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040629.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040629/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040629 none O=C([O-])CCOC1=CC=C(C=NNC(=O)CC(F)(F)F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [35, 24, 29, 16, 4, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 16, 68, 68, 68, 68, 1, 1, 24, 24, 16, 16, 1, 1, 6, 16, 68, 68, 1, 1] 201
rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 20, 21, 26, 27] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 28, 29, 30, 31])
total number of confs: 365
number of broken/clashed sets: 37
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040629 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040629
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040629/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040629
Building REAL300000040630
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040630'
/scratch/stefan/7769621/working/building/REAL300000040630 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040630

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040630/0 /scratch/stefan/7769621/working/building/REAL300000040630 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 728)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/728
`/scratch/stefan/7769621/working/3D/728' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(Br)C=C1C=NNC(=O)CC(F)(F)F)

`REAL300000040630.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040630.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040630/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040630 none O=C([O-])COC1=CC=C(Br)C=C1C=NNC(=O)CC(F)(F)F 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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, 8, 1, 11, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 49, 88, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 68, 68, 68, 68, 49, 49, 1, 1, 1, 6, 12, 68, 68] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30])
total number of confs: 513
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040630 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040630
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040630/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040630
Building REAL300000040631
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040631'
/scratch/stefan/7769621/working/building/REAL300000040631 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040631

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040631/0 /scratch/stefan/7769621/working/building/REAL300000040631 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 729)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/729
`/scratch/stefan/7769621/working/3D/729' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=CC(C=NNC(=O)CC(F)(F)F)=C1)C(=O)[O-])

`REAL300000040631.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040631.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040631/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040631 none CC(OC1=CC=CC(C=NNC(=O)CC(F)(F)F)=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.am', 'C.2', 'O.2', 'C.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, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [33, 11, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 11, 10, 53, 53, 53, 53, 1, 33, 49, 49, 33, 33, 33, 33, 1, 1, 1, 6, 10, 52, 52, 1] 201
rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 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])
total number of confs: 348
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040631 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040631
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040631/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040631
Building REAL300000040632
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040632'
/scratch/stefan/7769621/working/building/REAL300000040632 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040632

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040632/0 /scratch/stefan/7769621/working/building/REAL300000040632 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 730)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/730
`/scratch/stefan/7769621/working/3D/730' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=CC(C=NNC(=O)CC(F)(F)F)=C1)

`REAL300000040632.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040632.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040632/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040632 none O=C([O-])CCOC1=CC=CC(C=NNC(=O)CC(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 36, 46, 22, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 59, 60, 59, 60, 1, 36, 36, 22, 22, 1, 1, 1, 6, 11, 59, 59, 1] 201
rigid atoms, others: [33, 5, 6, 7, 8, 9, 10, 11, 21, 26, 27, 28] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31, 32])
total number of confs: 397
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040632 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040632
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040632/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040632
Building REAL300000040633
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040633'
/scratch/stefan/7769621/working/building/REAL300000040633 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040633

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040633/0 /scratch/stefan/7769621/working/building/REAL300000040633 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 731)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/731
`/scratch/stefan/7769621/working/3D/731' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC=C1COC1=CC(C=NNC(=O)CC(F)(F)F)=CC=C1)

`REAL300000040633.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040633.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040633/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040633 none O=C([O-])C1=CC=CC=C1COC1=CC(C=NNC(=O)CC(F)(F)F)=CC=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.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.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, 1, 1, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [15, 13, 15, 13, 13, 13, 13, 13, 5, 3, 1, 1, 1, 1, 1, 8, 8, 16, 16, 16, 56, 56, 56, 56, 1, 1, 1, 13, 13, 13, 13, 5, 5, 1, 8, 16, 56, 56, 1, 1, 1] 115
rigid atoms, others: [33, 38, 39, 40, 10, 11, 12, 13, 14, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 227
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040633 none O=C([O-])C1=CC=CC=C1COC1=CC(C=NNC(=O)CC(F)(F)F)=CC=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.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.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, 1, 1, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 7, 13, 13, 13, 32, 32, 46, 46, 46, 115, 115, 115, 115, 12, 13, 13, 1, 1, 1, 1, 5, 5, 13, 32, 46, 115, 115, 12, 13, 13] 115
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29, 30] set([0, 2, 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])
total number of confs: 435
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040633 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040633
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040633/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040633
Building REAL300000040634
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040634'
/scratch/stefan/7769621/working/building/REAL300000040634 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040634

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040634/0 /scratch/stefan/7769621/working/building/REAL300000040634 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 732)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/732
`/scratch/stefan/7769621/working/3D/732' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC(=O)CC(F)(F)F)C=C1[N+](=O)[O-])

`REAL300000040634.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040634.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040634/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040634 none O=C([O-])COC1=CC=C(C=NNC(=O)CC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 11, 5, 5, 15, 15, 15, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 25, 32, 7, 1, 1, 1, 1, 1, 1, 8, 8, 20, 20, 20, 85, 85, 85, 85, 1, 1, 1, 2, 2, 25, 25, 1, 1, 8, 20, 85, 85, 1] 201
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 19, 20, 21, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 28, 29, 30, 31])
total number of confs: 398
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040634 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040634
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040634/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040634
Building REAL300000040635
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040635'
/scratch/stefan/7769621/working/building/REAL300000040635 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040635

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040635/0 /scratch/stefan/7769621/working/building/REAL300000040635 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 733)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/733
`/scratch/stefan/7769621/working/3D/733' -> `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=NNC(=O)CC(F)(F)F)C=C2)=C1)

`REAL300000040635.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040635.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040635/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040635 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC(=O)CC(F)(F)F)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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 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, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 19, 19, 29, 29, 19, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 23, 23, 23, 53, 53, 53, 53, 1, 1, 19, 19, 19, 19, 5, 5, 1, 1, 11, 23, 53, 53, 1, 1, 19] 201
rigid atoms, others: [32, 33, 38, 39, 8, 9, 10, 11, 12, 13, 14, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 40])
total number of confs: 255
number of broken/clashed sets: 31
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040635 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC(=O)CC(F)(F)F)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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 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, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 19, 19, 19, 19, 19, 61, 61, 89, 89, 89, 201, 201, 201, 201, 19, 19, 1, 2, 2, 2, 9, 9, 19, 19, 61, 89, 201, 201, 18, 19, 1] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 40, 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])
total number of confs: 731
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040635 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040635
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040635/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040635
Building REAL300000040636
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040636'
/scratch/stefan/7769621/working/building/REAL300000040636 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040636

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040636/0 /scratch/stefan/7769621/working/building/REAL300000040636 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 734)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/734
`/scratch/stefan/7769621/working/3D/734' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(COC2=CC(C=NNC(=O)CC(F)(F)F)=CC=C2)=CC=C1)

`REAL300000040636.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040636.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040636/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040636 none O=C([O-])C1=CC(COC2=CC(C=NNC(=O)CC(F)(F)F)=CC=C2)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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: [11, 1, 11, 1, 1, 1, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 19, 19, 19, 5, 3, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 34, 34, 34, 34, 1, 1, 1, 19, 19, 19, 19, 5, 5, 1, 6, 10, 34, 34, 1, 1, 1, 19, 19, 19] 201
rigid atoms, others: [35, 36, 37, 7, 8, 9, 10, 11, 21, 22, 23, 30] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 38, 39, 40])
total number of confs: 151
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040636 none O=C([O-])C1=CC(COC2=CC(C=NNC(=O)CC(F)(F)F)=CC=C2)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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: [11, 1, 11, 1, 1, 1, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 8, 10, 19, 19, 19, 69, 69, 99, 99, 99, 201, 201, 201, 201, 18, 19, 19, 1, 1, 1, 1, 8, 8, 19, 69, 99, 201, 201, 18, 19, 19, 1, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 39, 38, 40, 24, 25, 26, 27] set([0, 2, 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])
total number of confs: 736
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040636 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040636
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040636/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040636
Building REAL300000040637
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040637'
/scratch/stefan/7769621/working/building/REAL300000040637 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040637

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040637/0 /scratch/stefan/7769621/working/building/REAL300000040637 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 735)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/735
`/scratch/stefan/7769621/working/3D/735' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=CC(C=NNC(=O)CC(F)(F)F)=C1)

`REAL300000040637.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040637.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040637/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040637 none O=C([O-])COC1=CC=CC(C=NNC(=O)CC(F)(F)F)=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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', '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, 8, 1, 11, 5, 5, 15, 15, 15, 1, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 23, 38, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 14, 14, 14, 65, 66, 65, 66, 1, 23, 23, 1, 1, 1, 8, 14, 65, 65, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 20, 23, 24, 25, 30] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 26, 27, 28, 29])
total number of confs: 341
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040637 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040637
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040637/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040637
Building REAL300000040638
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040638'
/scratch/stefan/7769621/working/building/REAL300000040638 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040638

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040638/0 /scratch/stefan/7769621/working/building/REAL300000040638 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 736)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/736
`/scratch/stefan/7769621/working/3D/736' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(COC2=CC=C(C=NNC(=O)CC(F)(F)F)C=C2)OC=C1)

`REAL300000040638.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040638.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040638/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040638 none O=C([O-])C1=C(COC2=CC=C(C=NNC(=O)CC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [15, 12, 15, 11, 5, 1, 1, 1, 1, 1, 1, 1, 9, 9, 19, 19, 19, 49, 49, 49, 49, 1, 1, 11, 11, 11, 5, 5, 1, 1, 9, 19, 49, 49, 1, 1, 11, 11] 113
rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 11, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 36, 37])
total number of confs: 215
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040638 none O=C([O-])C1=C(COC2=CC=C(C=NNC(=O)CC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 5, 11, 11, 11, 11, 11, 31, 31, 41, 41, 41, 113, 113, 113, 113, 11, 11, 1, 1, 1, 5, 5, 11, 11, 31, 41, 113, 113, 11, 11, 1, 1] 113
rigid atoms, others: [1, 3, 4, 5, 23, 24, 25, 37, 36] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 413
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040638 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040638
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040638/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040638
Building REAL300000040639
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040639'
/scratch/stefan/7769621/working/building/REAL300000040639 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040639

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040639/0 /scratch/stefan/7769621/working/building/REAL300000040639 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 737)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/737
`/scratch/stefan/7769621/working/3D/737' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNC(=O)CC(F)(F)F)C(OCC(=O)[O-])=C1)

`REAL300000040639.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040639.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040639/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040639 none COC1=CC=C(C=NNC(=O)CC(F)(F)F)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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 12, 5, 1, 11, 11, 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, 4, 7, 6, 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
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, 8, 8, 39, 39, 39, 39, 1, 1, 9, 43, 71, 71, 1, 3, 3, 3, 1, 1, 4, 8, 39, 39, 43, 43, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 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])
total number of confs: 374
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040639 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040639
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040639/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040639
Building REAL300000040640
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040640'
/scratch/stefan/7769621/working/building/REAL300000040640 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040640

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040640/0 /scratch/stefan/7769621/working/building/REAL300000040640 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 738)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/738
`/scratch/stefan/7769621/working/3D/738' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C(F)(F)OC1=CC=C(C=NNC(=O)CC(F)(F)F)C=C1)

`REAL300000040640.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040640.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040640/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040640 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC(=O)CC(F)(F)F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [45, 29, 45, 7, 29, 29, 1, 1, 1, 1, 1, 1, 6, 6, 12, 13, 12, 50, 50, 50, 50, 1, 1, 1, 1, 6, 12, 49, 49, 1, 1] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28])
total number of confs: 325
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040640 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040640
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040640/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040640
Building REAL300000040641
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040641'
/scratch/stefan/7769621/working/building/REAL300000040641 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040641

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040641/0 /scratch/stefan/7769621/working/building/REAL300000040641 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 739)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/739
`/scratch/stefan/7769621/working/3D/739' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(C(=O)[O-])=CC(Br)=C1C=NNC(=O)CC(F)(F)F)

`REAL300000040641.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040641.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040641/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040641 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC(=O)CC(F)(F)F 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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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, 1, 11, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 12, 12, 25, 25, 25, 56, 56, 56, 56, 2, 2, 2, 1, 12, 25, 56, 56] 56
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])
total number of confs: 208
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040641 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040641
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040641/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040641
Building REAL300000040642
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040642'
/scratch/stefan/7769621/working/building/REAL300000040642 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040642

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040642/0 /scratch/stefan/7769621/working/building/REAL300000040642 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 740)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/740
`/scratch/stefan/7769621/working/3D/740' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC(=O)CC(F)(F)F)C=C1Br)

`REAL300000040642.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040642.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040642/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040642 none O=C([O-])COC1=CC=C(C=NNC(=O)CC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Br', '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, 11, 5, 5, 15, 15, 15, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 34, 59, 8, 1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 59, 59, 59, 59, 1, 1, 1, 34, 34, 1, 1, 6, 15, 59, 59, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 19, 20, 21, 24, 25, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27, 28, 29])
total number of confs: 393
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040642 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040642
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040642/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040642
Building REAL300000040643
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040643'
/scratch/stefan/7769621/working/building/REAL300000040643 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040643

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040643/0 /scratch/stefan/7769621/working/building/REAL300000040643 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 741)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/741
`/scratch/stefan/7769621/working/3D/741' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC(=O)CC(F)(F)F)C=C1)

`REAL300000040643.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040643.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040643/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040643 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC(=O)CC(F)(F)F)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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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, 1, 11, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 6, 6, 8, 8, 8, 43, 43, 43, 43, 1, 1, 3, 3, 3, 1, 6, 8, 43, 43, 1, 1] 43
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 9, 10, 11, 12, 22, 23, 27] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29, 30, 31])
total number of confs: 146
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040643 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040643
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040643/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040643
Building REAL300000040644
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040644'
/scratch/stefan/7769621/working/building/REAL300000040644 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040644

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040644/0 /scratch/stefan/7769621/working/building/REAL300000040644 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 742)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/742
`/scratch/stefan/7769621/working/3D/742' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC(=O)CC(F)(F)F)C1=CC=C(C(=O)[O-])C=C1)

`REAL300000040644.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040644.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040644/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040644 none CCC(=NNC(=O)CC(F)(F)F)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 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
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [17, 7, 1, 7, 7, 26, 26, 26, 61, 61, 61, 61, 1, 1, 1, 1, 1, 2, 2, 1, 1, 17, 17, 17, 17, 17, 26, 61, 61, 1, 1, 1, 1] 70
rigid atoms, others: [32, 2, 12, 13, 14, 15, 16, 19, 20, 29, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 273
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040644 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040644
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040644/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040644
Building REAL300000040645
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040645'
/scratch/stefan/7769621/working/building/REAL300000040645 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040645

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040645/0 /scratch/stefan/7769621/working/building/REAL300000040645 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 743)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/743
`/scratch/stefan/7769621/working/3D/743' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)CC(F)(F)F)C1=CC(C(=O)[O-])=CC=C1O)

`REAL300000040645.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040645.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040645/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040645 none CC(=NNC(=O)CC(F)(F)F)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 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, 29, 29, 29, 64, 64, 64, 64, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 10, 10, 10, 29, 64, 64, 1, 1, 1, 2] 128
rigid atoms, others: [1, 11, 12, 13, 14, 17, 18, 19, 20, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 227
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040645 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040645
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040645/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040645
Building REAL300000040646
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040646'
/scratch/stefan/7769621/working/building/REAL300000040646 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040646

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040646/0 /scratch/stefan/7769621/working/building/REAL300000040646 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 744)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/744
`/scratch/stefan/7769621/working/3D/744' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC(=O)CC(F)(F)F)C1=CC(C(=O)[O-])=CC=C1F)

`REAL300000040646.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040646.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040646/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040646 none CCC(=NNC(=O)CC(F)(F)F)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 12, 1, 12, 12, 55, 55, 55, 137, 137, 137, 137, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 31, 31, 31, 31, 31, 55, 137, 137, 1, 1, 1] 143
rigid atoms, others: [32, 2, 12, 13, 14, 15, 18, 19, 20, 21, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 593
number of broken/clashed sets: 55
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040646 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040646
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040646/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040646
Building REAL300000040647
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040647'
/scratch/stefan/7769621/working/building/REAL300000040647 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040647

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040647/0 /scratch/stefan/7769621/working/building/REAL300000040647 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 745)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/745
`/scratch/stefan/7769621/working/3D/745' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=NNC(C=NNC(=O)CC(F)(F)F)=C2C=C1)

`REAL300000040647.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040647.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040647/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040647 none O=C([O-])C1=CC2=NNC(C=NNC(=O)CC(F)(F)F)=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 29, 29, 29, 29, 1, 1, 1, 1, 1, 4, 8, 29, 29, 1, 1] 29
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 28, 29] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27])
total number of confs: 99
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040647 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040647/1 /scratch/stefan/7769621/working/building/REAL300000040647 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 746)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/746
`/scratch/stefan/7769621/working/3D/746' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(C=NNC(=O)CC(F)(F)F)=NNC2=C1)

`REAL300000040647.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040647.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040647/1/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: REAL300000040647 none O=C([O-])C1=CC=C2C(C=NNC(=O)CC(F)(F)F)=NNC2=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', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 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, 1, 9, 9, 22, 22, 22, 52, 52, 52, 52, 1, 1, 1, 1, 1, 1, 9, 22, 52, 52, 1, 1] 53
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 28, 29] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27])
total number of confs: 186
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040647 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040647
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040647/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040647/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040647
Building REAL300000040648
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040648'
/scratch/stefan/7769621/working/building/REAL300000040648 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040648

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040648/0 /scratch/stefan/7769621/working/building/REAL300000040648 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 747)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/747
`/scratch/stefan/7769621/working/3D/747' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)CC(F)(F)F)C1=CC=C(C(=O)[O-])C(F)=C1)

`REAL300000040648.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040648.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040648/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040648 none CC(=NNC(=O)CC(F)(F)F)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 38, 38, 38, 114, 114, 114, 114, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 11, 11, 11, 38, 114, 114, 1, 1, 1] 114
rigid atoms, others: [1, 11, 12, 13, 14, 15, 18, 19, 20, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 21, 22, 23, 24, 25, 26])
total number of confs: 394
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040648 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040648
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040648/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040648
Building REAL300000040649
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040649'
/scratch/stefan/7769621/working/building/REAL300000040649 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040649

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040649/0 /scratch/stefan/7769621/working/building/REAL300000040649 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 748)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/748
`/scratch/stefan/7769621/working/3D/748' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)CC(F)(F)F)=C([N+](=O)[O-])C=C1OCC(=O)[O-])

`REAL300000040649.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040649.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040649/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040649 none COC1=CC(C=NNC(=O)CC(F)(F)F)=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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 7, 7, 7, 36, 36, 36, 36, 1, 1, 2, 2, 1, 1, 1, 10, 40, 56, 56, 4, 4, 4, 1, 5, 7, 36, 36, 1, 40, 40] 201
rigid atoms, others: [1, 2, 3, 4, 5, 34, 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, 35, 36])
total number of confs: 323
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040649 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040649
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040649/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040649
Building REAL300000040650
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040650'
/scratch/stefan/7769621/working/building/REAL300000040650 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040650

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040650/0 /scratch/stefan/7769621/working/building/REAL300000040650 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 749)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/749
`/scratch/stefan/7769621/working/3D/749' -> `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=NNC(=O)CC(F)(F)F)

`REAL300000040650.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040650.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040650/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040650 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNC(=O)CC(F)(F)F 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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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, 1, 11, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 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: [2, 1, 2, 5, 6, 6, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 3, 3, 4, 4, 4, 15, 15, 15, 15, 2, 2, 2, 5, 5, 1, 1, 1, 3, 4, 15, 15] 18
rigid atoms, others: [32, 1, 33, 6, 7, 8, 9, 10, 14, 15, 16, 31] set([0, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37])
total number of confs: 79
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040650 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040650
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040650/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040650
Building REAL300000040651
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040651'
/scratch/stefan/7769621/working/building/REAL300000040651 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040651

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040651/0 /scratch/stefan/7769621/working/building/REAL300000040651 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 750)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/750
`/scratch/stefan/7769621/working/3D/750' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)CC(F)(F)F)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1)

`REAL300000040651.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040651.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040651/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040651 none CC(=NNC(=O)CC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 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, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [65, 19, 65, 65, 99, 99, 99, 201, 201, 201, 201, 5, 19, 19, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 19, 19, 65, 65, 65, 99, 201, 201, 19, 19, 1, 1, 1, 1, 19, 19] 201
rigid atoms, others: [35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40])
total number of confs: 771
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040651 none CC(=NNC(=O)CC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 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, 6, 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
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, 20, 20, 20, 70, 70, 70, 70, 1, 1, 1, 1, 1, 9, 19, 19, 12, 19, 19, 19, 19, 19, 1, 1, 6, 6, 6, 20, 70, 70, 1, 1, 19, 19, 19, 19, 1, 1] 201
rigid atoms, others: [1, 34, 33, 40, 11, 12, 13, 14, 15, 25, 26, 39] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38])
total number of confs: 294
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040651 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040651
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040651/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040651
Building REAL300000040652
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040652'
/scratch/stefan/7769621/working/building/REAL300000040652 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040652

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040652/0 /scratch/stefan/7769621/working/building/REAL300000040652 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 751)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/751
`/scratch/stefan/7769621/working/3D/751' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)CC(F)(F)F)=CC=C1OCCC(=O)[O-])

`REAL300000040652.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040652.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040652/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040652 none COC1=CC(C=NNC(=O)CC(F)(F)F)=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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 7, 7, 37, 37, 37, 37, 1, 1, 1, 1, 9, 43, 53, 75, 68, 3, 3, 3, 1, 7, 7, 37, 37, 1, 1, 43, 43, 53, 53] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 33, 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, 34, 35, 36, 37])
total number of confs: 390
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040652 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040652
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040652/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040652
Building REAL300000040653
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040653'
/scratch/stefan/7769621/working/building/REAL300000040653 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040653

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040653/0 /scratch/stefan/7769621/working/building/REAL300000040653 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 752)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/752
`/scratch/stefan/7769621/working/3D/752' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC(=O)CC(F)(F)F)C(Cl)=C1)

`REAL300000040653.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040653.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040653/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040653 none O=C([O-])C1=CC=C(C=NNC(=O)CC(F)(F)F)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 10, 16, 16, 16, 34, 34, 34, 34, 1, 1, 1, 1, 1, 10, 16, 34, 34, 1] 34
rigid atoms, others: [1, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25])
total number of confs: 130
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040653 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040653
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040653/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040653
Building REAL300000040654
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040654'
/scratch/stefan/7769621/working/building/REAL300000040654 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040654

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040654/0 /scratch/stefan/7769621/working/building/REAL300000040654 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 753)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/753
`/scratch/stefan/7769621/working/3D/753' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)CC(F)(F)F)C1=CC(C(=O)[O-])=C(C)N=C1C)

`REAL300000040654.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040654.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040654/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040654 none CC(=NNC(=O)CC(F)(F)F)C1=CC(C(=O)[O-])=C(C)N=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
84  conformations in input
total number of sets (complete confs): 84
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 23, 23, 23, 84, 84, 84, 84, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 9, 9, 9, 23, 84, 84, 1, 2, 2, 2, 2, 2, 2] 84
rigid atoms, others: [1, 11, 12, 13, 14, 17, 18, 19, 20, 21, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34])
total number of confs: 318
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040654 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040654
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040654/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040654
Building REAL300000040655
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040655'
/scratch/stefan/7769621/working/building/REAL300000040655 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040655

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040655/0 /scratch/stefan/7769621/working/building/REAL300000040655 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 754)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/754
`/scratch/stefan/7769621/working/3D/754' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)CC(F)(F)F)C1=CC(C(=O)[O-])=CC=C1C)

`REAL300000040655.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040655.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040655/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040655 none CC(=NNC(=O)CC(F)(F)F)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 1, 9, 9, 18, 18, 18, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 18, 43, 43, 1, 1, 1, 2, 2, 2] 43
rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 154
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040655 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040655
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040655/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040655
Building REAL300000040656
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040656'
/scratch/stefan/7769621/working/building/REAL300000040656 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040656

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040656/0 /scratch/stefan/7769621/working/building/REAL300000040656 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 755)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/755
`/scratch/stefan/7769621/working/3D/755' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=C(C=NNC(=O)CC(F)(F)F)C=C1)C(=O)[O-])

`REAL300000040656.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040656.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040656/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040656 none CC(OC1=CC=C(C=NNC(=O)CC(F)(F)F)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.am', 'C.2', 'O.2', 'C.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', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 6, 1, 1, 1, 1, 1, 1, 11, 11, 22, 22, 22, 91, 91, 91, 91, 1, 1, 20, 32, 32, 20, 20, 20, 20, 1, 1, 11, 22, 91, 91, 1, 1] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 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])
total number of confs: 417
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040656 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040656
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040656/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040656
Building REAL300000040657
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040657'
/scratch/stefan/7769621/working/building/REAL300000040657 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040657

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040657/0 /scratch/stefan/7769621/working/building/REAL300000040657 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 756)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/756
`/scratch/stefan/7769621/working/3D/756' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1CCC(=NNC(=O)CC(F)(F)F)C2=CC=CC=C21)

`REAL300000040657.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040657.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040657/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040657 none O=C([O-])C1CCC(=NNC(=O)CC(F)(F)F)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 8, 8, 8, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 17, 17, 1, 1, 1, 1] 17
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29])
total number of confs: 60
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040657 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040657
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040657/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040657
Building REAL300000040658
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040658'
/scratch/stefan/7769621/working/building/REAL300000040658 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040658

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040658/0 /scratch/stefan/7769621/working/building/REAL300000040658 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 757)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/757
`/scratch/stefan/7769621/working/3D/757' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CN1C=C(C=NNC(=O)CC(F)(F)F)C2=CC=CC=C21)

`REAL300000040658.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040658.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040658/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040658 none O=C([O-])CN1C=C(C=NNC(=O)CC(F)(F)F)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.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, 8, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 15, 1, 1, 1, 1, 1, 12, 12, 33, 33, 32, 128, 128, 128, 128, 1, 1, 1, 1, 1, 1, 8, 8, 1, 12, 32, 127, 127, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 25, 30, 31] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 26, 27, 28, 29])
total number of confs: 488
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040658 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040658
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040658/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040658
Building REAL300000040659
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040659'
/scratch/stefan/7769621/working/building/REAL300000040659 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040659

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040659/0 /scratch/stefan/7769621/working/building/REAL300000040659 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 758)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/758
`/scratch/stefan/7769621/working/3D/758' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)CC(F)(F)F)C1=CC=CC(OCCCC(=O)[O-])=C1)

`REAL300000040659.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040659.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040659/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040659 none CC(=NNC(=O)CC(F)(F)F)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 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]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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
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, 11, 11, 11, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 7, 27, 41, 59, 75, 75, 1, 9, 9, 9, 11, 27, 27, 1, 1, 1, 27, 27, 41, 41, 59, 59, 1] 201
rigid atoms, others: [32, 1, 39, 11, 12, 13, 14, 15, 16, 23, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38])
total number of confs: 401
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040659 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040659
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040659/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040659
Building REAL300000040660
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040660'
/scratch/stefan/7769621/working/building/REAL300000040660 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040660

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040660/0 /scratch/stefan/7769621/working/building/REAL300000040660 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 759)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/759
`/scratch/stefan/7769621/working/3D/759' -> `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)=NNC(=O)CC(F)(F)F)

`REAL300000040660.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040660.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040660/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040660 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)=NNC(=O)CC(F)(F)F 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', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 1, 1, 1, 1, 1, 1, 1, 9, 24, 24, 30, 30, 1, 1, 7, 7, 16, 16, 16, 61, 61, 61, 61, 7, 7, 7, 3, 3, 1, 1, 1, 1, 24, 24, 24, 24, 1, 1, 16, 61, 61] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 39, 14, 15, 38, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 40, 41, 42])
total number of confs: 324
number of broken/clashed sets: 193
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040660 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040660
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040660/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040660
Building REAL300000040661
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040661'
/scratch/stefan/7769621/working/building/REAL300000040661 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040661

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040661/0 /scratch/stefan/7769621/working/building/REAL300000040661 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 760)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/760
`/scratch/stefan/7769621/working/3D/760' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CC=C(OCC(=O)[O-])C=C1)=NNC(=O)CC(F)(F)F)

`REAL300000040661.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040661.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040661/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040661 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)=NNC(=O)CC(F)(F)F 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 4, 2, 1, 1, 1, 1, 1, 1, 6, 18, 30, 30, 1, 1, 9, 9, 16, 16, 16, 50, 50, 50, 50, 9, 9, 9, 4, 4, 2, 2, 1, 1, 18, 18, 1, 1, 16, 50, 50] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 13, 14, 35, 36, 31] set([0, 1, 2, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37, 38, 39])
total number of confs: 270
number of broken/clashed sets: 200
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040661 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040661
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040661/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040661
Building REAL300000040662
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040662'
/scratch/stefan/7769621/working/building/REAL300000040662 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040662

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040662/0 /scratch/stefan/7769621/working/building/REAL300000040662 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 761)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/761
`/scratch/stefan/7769621/working/3D/761' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)CC(F)(F)F)C1=CC=CC(OC(C)C(=O)[O-])=C1)

`REAL300000040662.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040662.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040662/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040662 none CC(=NNC(=O)CC(F)(F)F)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 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]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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: [9, 1, 9, 9, 14, 14, 14, 55, 55, 55, 55, 1, 1, 1, 1, 1, 1, 11, 26, 26, 39, 39, 1, 9, 9, 9, 14, 55, 55, 1, 1, 1, 26, 26, 26, 26, 1] 201
rigid atoms, others: [1, 36, 11, 12, 13, 14, 15, 16, 22, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35])
total number of confs: 319
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040662 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040662
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040662/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040662
Building REAL300000040663
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040663'
/scratch/stefan/7769621/working/building/REAL300000040663 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040663

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040663/0 /scratch/stefan/7769621/working/building/REAL300000040663 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 762)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/762
`/scratch/stefan/7769621/working/3D/762' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)=NNC(=O)CC(F)(F)F)

`REAL300000040663.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040663.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040663/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040663 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)=NNC(=O)CC(F)(F)F 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', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 3, 1, 1, 1, 1, 1, 1, 1, 6, 20, 26, 38, 33, 1, 1, 9, 9, 19, 19, 19, 47, 47, 47, 47, 9, 9, 9, 3, 3, 1, 1, 1, 1, 20, 20, 26, 26, 1, 1, 19, 47, 47] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 39, 14, 15, 38, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 40, 41, 42])
total number of confs: 335
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040663 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040663
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040663/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040663
Building REAL300000040664
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040664'
/scratch/stefan/7769621/working/building/REAL300000040664 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040664

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040664/0 /scratch/stefan/7769621/working/building/REAL300000040664 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 763)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/763
`/scratch/stefan/7769621/working/3D/763' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC(=O)CC(F)(F)F)C1=CC=C(OCCCCC(=O)[O-])C=C1)

`REAL300000040664.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040664.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040664/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040664 none CCC(=NNC(=O)CC(F)(F)F)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 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]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 1, 7, 7, 12, 12, 12, 31, 31, 31, 31, 1, 1, 1, 1, 1, 6, 11, 23, 29, 48, 55, 58, 1, 1, 10, 10, 10, 10, 10, 12, 31, 31, 1, 1, 11, 11, 23, 23, 30, 30, 47, 47, 1, 1] 201
rigid atoms, others: [2, 35, 44, 45, 12, 34, 14, 13, 16, 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, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 387
number of broken/clashed sets: 50
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040664 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040664
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040664/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040664
Building REAL300000040665
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040665'
/scratch/stefan/7769621/working/building/REAL300000040665 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040665

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040665/0 /scratch/stefan/7769621/working/building/REAL300000040665 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 764)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/764
`/scratch/stefan/7769621/working/3D/764' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1(C2=CC=CC=C2)CC(=NNC(=O)CC(F)(F)F)C1)

`REAL300000040665.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040665.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040665/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040665 none O=C([O-])C1(C2=CC=CC=C2)CC(=NNC(=O)CC(F)(F)F)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.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', '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, 5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [6, 4, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 11, 11, 53, 53, 53, 53, 4, 1, 1, 1, 1, 1, 4, 4, 11, 53, 53, 4, 4] 53
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 181
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040665 none O=C([O-])C1(C2=CC=CC=C2)CC(=NNC(=O)CC(F)(F)F)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.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', '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, 5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 4, 4, 1, 4, 4, 1, 1, 1, 1, 5, 5, 5, 32, 32, 32, 32, 1, 4, 4, 1, 4, 4, 1, 1, 5, 32, 32, 1, 1] 53
rigid atoms, others: [32, 1, 3, 4, 33, 10, 11, 12, 13, 21, 27, 28] set([0, 2, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31])
total number of confs: 119
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040665 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040665
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040665/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040665
Building REAL300000040666
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040666'
/scratch/stefan/7769621/working/building/REAL300000040666 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040666

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040666/0 /scratch/stefan/7769621/working/building/REAL300000040666 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 765)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/765
`/scratch/stefan/7769621/working/3D/765' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)CC(F)(F)F)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C)

`REAL300000040666.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040666.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040666/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040666 none CC(=NNC(=O)CC(F)(F)F)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 4, 11, 11, 11, 36, 36, 36, 36, 1, 1, 1, 1, 1, 1, 6, 8, 8, 1, 1, 1, 4, 4, 4, 11, 36, 36, 1, 1, 6, 6, 2, 2, 2, 2, 2, 2] 44
rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 20, 21, 22, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 162
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040666 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040666
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040666/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040666
Building REAL300000040667
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040667'
/scratch/stefan/7769621/working/building/REAL300000040667 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040667

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040667/0 /scratch/stefan/7769621/working/building/REAL300000040667 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 766)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/766
`/scratch/stefan/7769621/working/3D/766' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(=NNC(=O)CC(F)(F)F)CCC(C(=O)[O-])C1(C)C)

`REAL300000040667.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040667.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040667/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040667 none CC1C(=NNC(=O)CC(F)(F)F)CCC(C(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 15, 15, 15, 15, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 2, 1, 7, 15, 15, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 15
rigid atoms, others: [0, 1, 2, 3, 4, 32, 12, 13, 14, 15, 18, 19, 20, 24, 28, 29, 30, 31] set([33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 38, 16, 17, 21, 22, 23, 25, 26, 27, 37])
total number of confs: 73
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040667 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040667
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040667/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040667
Building REAL300000040668
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040668'
/scratch/stefan/7769621/working/building/REAL300000040668 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040668

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040668/0 /scratch/stefan/7769621/working/building/REAL300000040668 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 767)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/767
`/scratch/stefan/7769621/working/3D/767' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(C)=NNC(=O)CC(F)(F)F)=CC=C1OCCCC(=O)[O-])

`REAL300000040668.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040668.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040668/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040668 none COC1=CC(C(C)=NNC(=O)CC(F)(F)F)=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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 11, 5, 5, 15, 15, 15, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 6, 15, 15, 15, 57, 57, 57, 57, 1, 1, 1, 1, 9, 19, 23, 35, 46, 46, 4, 4, 4, 1, 7, 7, 7, 15, 57, 57, 1, 1, 19, 19, 23, 23, 35, 35] 201
rigid atoms, others: [1, 2, 3, 4, 5, 16, 17, 18, 19, 36, 29, 37] 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, 38, 39, 40, 41, 42, 43])
total number of confs: 417
number of broken/clashed sets: 199
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040668 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040668
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040668/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040668
Building REAL300000040669
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040669'
/scratch/stefan/7769621/working/building/REAL300000040669 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040669

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040669/0 /scratch/stefan/7769621/working/building/REAL300000040669 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 768)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/768
`/scratch/stefan/7769621/working/3D/768' -> `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(=NNC(=O)CC(F)(F)F)C1)

`REAL300000040669.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040669.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040669/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040669 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(=NNC(=O)CC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', '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, 8, 1, 11, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [15, 9, 15, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 22, 22, 22, 75, 75, 75, 75, 9, 1, 1, 1, 1, 9, 9, 22, 75, 75, 9, 9] 75
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 279
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040669 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(=NNC(=O)CC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', '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, 8, 1, 11, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 9, 9, 4, 9, 9, 9, 1, 1, 1, 1, 5, 5, 5, 38, 38, 38, 38, 1, 9, 9, 7, 9, 1, 1, 5, 38, 38, 1, 1] 75
rigid atoms, others: [32, 1, 3, 4, 33, 11, 12, 13, 14, 22, 27, 28] set([0, 2, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31])
total number of confs: 157
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040669 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040669
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040669/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040669
Building REAL300000040670
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040670'
/scratch/stefan/7769621/working/building/REAL300000040670 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040670

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040670/0 /scratch/stefan/7769621/working/building/REAL300000040670 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 769)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/769
`/scratch/stefan/7769621/working/3D/769' -> `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(=NNC(=O)CC(F)(F)F)C1)

`REAL300000040670.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040670.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040670/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040670 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(=NNC(=O)CC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', '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, 8, 1, 11, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
79  conformations in input
total number of sets (complete confs): 79
using faster count positions algorithm for large data
unique positions, atoms: [17, 11, 17, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 25, 25, 25, 79, 79, 79, 79, 11, 1, 1, 1, 1, 11, 11, 25, 79, 79, 11, 11] 79
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 291
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040670 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(=NNC(=O)CC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', '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, 8, 1, 11, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
79  conformations in input
total number of sets (complete confs): 79
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 11, 11, 1, 11, 11, 11, 1, 1, 1, 1, 5, 5, 5, 38, 38, 38, 38, 1, 11, 11, 9, 11, 1, 1, 5, 38, 38, 1, 1] 79
rigid atoms, others: [32, 1, 3, 4, 33, 11, 12, 13, 14, 22, 27, 28] set([0, 2, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31])
total number of confs: 163
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040670 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040670
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040670/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040670
Building REAL300000040671
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040671'
/scratch/stefan/7769621/working/building/REAL300000040671 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040671

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040671/0 /scratch/stefan/7769621/working/building/REAL300000040671 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 770)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/770
`/scratch/stefan/7769621/working/3D/770' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC(=O)CC(F)(F)F)

`REAL300000040671.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040671.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040671/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040671 none O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC(=O)CC(F)(F)F 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', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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, 5, 5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 18, 18] 18
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([32, 33, 15, 16, 17, 18, 19, 20, 21, 31])
total number of confs: 63
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040671 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040671
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040671/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040671
Building REAL300000040672
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040672'
/scratch/stefan/7769621/working/building/REAL300000040672 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040672

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040672/0 /scratch/stefan/7769621/working/building/REAL300000040672 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 771)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/771
`/scratch/stefan/7769621/working/3D/771' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)CC(F)(F)F)C1=CC(Br)=CC=C1OCC(=O)[O-])

`REAL300000040672.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040672.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040672/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040672 none CC(=NNC(=O)CC(F)(F)F)C1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [9, 1, 9, 9, 19, 19, 19, 86, 86, 86, 86, 1, 1, 1, 1, 1, 1, 1, 1, 9, 43, 72, 72, 9, 9, 9, 19, 86, 86, 1, 1, 1, 43, 43] 201
rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33])
total number of confs: 519
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040672 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040672
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040672/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040672
Building REAL300000040673
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040673'
/scratch/stefan/7769621/working/building/REAL300000040673 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040673

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040673/0 /scratch/stefan/7769621/working/building/REAL300000040673 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 772)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/772
`/scratch/stefan/7769621/working/3D/772' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)CC(F)(F)F)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1)

`REAL300000040673.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040673.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040673/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040673 none CC(=NNC(=O)CC(F)(F)F)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 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]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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]
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: [9, 1, 9, 9, 25, 25, 25, 59, 59, 59, 59, 1, 1, 1, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 25, 59, 59, 2, 2, 1, 1, 2, 2, 2, 1] 59
rigid atoms, others: [1, 34, 38, 33, 11, 12, 13, 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, 35, 36, 37])
total number of confs: 233
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040673 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040673
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040673/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040673
Building REAL300000040674
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040674'
/scratch/stefan/7769621/working/building/REAL300000040674 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040674

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040674/0 /scratch/stefan/7769621/working/building/REAL300000040674 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 773)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/773
`/scratch/stefan/7769621/working/3D/773' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC(=O)CC(F)(F)F)

`REAL300000040674.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040674.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040674/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040674 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC(=O)CC(F)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 12, 12, 32, 32, 32, 61, 61, 61, 61, 2, 2, 2, 1, 2, 2, 2, 1, 12, 32, 61, 61] 61
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 24, 28] set([32, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31])
total number of confs: 244
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040674 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040674
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040674/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040674
Building REAL300000040675
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040675'
/scratch/stefan/7769621/working/building/REAL300000040675 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040675

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040675/0 /scratch/stefan/7769621/working/building/REAL300000040675 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 774)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/774
`/scratch/stefan/7769621/working/3D/774' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Cl)C(C=NNC(=O)CC(F)(F)F)=CC=C1)

`REAL300000040675.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040675.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040675/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040675 none O=C([O-])C1=C(Cl)C(C=NNC(=O)CC(F)(F)F)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 34, 34, 34, 34, 1, 1, 1, 4, 10, 34, 34, 1, 1, 1] 34
rigid atoms, others: [1, 3, 4, 5, 6, 7, 17, 18, 19, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23])
total number of confs: 120
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040675 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040675
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040675/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040675
Building REAL300000040676
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040676'
/scratch/stefan/7769621/working/building/REAL300000040676 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040676

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040676/0 /scratch/stefan/7769621/working/building/REAL300000040676 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 775)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/775
`/scratch/stefan/7769621/working/3D/775' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC(=O)CC(F)(F)F)

`REAL300000040676.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040676.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040676/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040676 none O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC(=O)CC(F)(F)F 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', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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, 5, 5, 5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 14, 14] 15
rigid atoms, others: [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] set([34, 35, 36, 16, 17, 18, 19, 20, 21, 22])
total number of confs: 48
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040676 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040676
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040676/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040676
Building REAL300000040677
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040677'
/scratch/stefan/7769621/working/building/REAL300000040677 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040677

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040677/0 /scratch/stefan/7769621/working/building/REAL300000040677 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 776)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/776
`/scratch/stefan/7769621/working/3D/776' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C(OC1=CC(C=NNC(=O)CC(F)(F)F)=CC=C1)C1=CC=CC=C1)

`REAL300000040677.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040677.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040677/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040677 none O=C([O-])C(OC1=CC(C=NNC(=O)CC(F)(F)F)=CC=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.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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: [11, 1, 11, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 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: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 39, 39, 39, 68, 68, 80, 80, 80, 201, 201, 201, 201, 39, 39, 39, 1, 1, 1, 1, 1, 1, 3, 39, 68, 80, 201, 201, 39, 39, 39, 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: 712
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040677 none O=C([O-])C(OC1=CC(C=NNC(=O)CC(F)(F)F)=CC=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.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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: [11, 1, 11, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 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: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 30, 38, 11, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 38, 38, 38, 38, 1, 1, 1, 30, 39, 39, 30, 39, 39, 30, 1, 4, 8, 38, 38, 1, 1, 1, 39, 39, 30, 39, 39] 201
rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 18, 19, 20, 28] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 36, 37, 38, 39, 40])
total number of confs: 306
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040677 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040677
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040677/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040677
Building REAL300000040678
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040678'
/scratch/stefan/7769621/working/building/REAL300000040678 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040678

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040678/0 /scratch/stefan/7769621/working/building/REAL300000040678 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 777)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/777
`/scratch/stefan/7769621/working/3D/777' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)CC(F)(F)F)C1=CC(C(=O)[O-])=CC=C1OC(C)C)

`REAL300000040678.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040678.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040678/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040678 none CC(=NNC(=O)CC(F)(F)F)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 10, 10, 30, 30, 30, 135, 135, 135, 135, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 19, 19, 10, 10, 10, 30, 135, 135, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19] 201
rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 512
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040678 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040678
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040678/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040678
Building REAL300000040679
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040679'
/scratch/stefan/7769621/working/building/REAL300000040679 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040679

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040679/0 /scratch/stefan/7769621/working/building/REAL300000040679 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 778)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/778
`/scratch/stefan/7769621/working/3D/778' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C2C(=CC=C1)CCC2=NNC(=O)CC(F)(F)F)

`REAL300000040679.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040679.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040679/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040679 none O=C([O-])C1=C2C(=CC=C1)CCC2=NNC(=O)CC(F)(F)F 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', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 1, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 5, 18, 18] 19
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30])
total number of confs: 69
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040679 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040679
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040679/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040679
Building REAL300000040680
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040680'
/scratch/stefan/7769621/working/building/REAL300000040680 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040680

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040680/0 /scratch/stefan/7769621/working/building/REAL300000040680 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 779)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/779
`/scratch/stefan/7769621/working/3D/779' -> `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=NNC(=O)CC(F)(F)F)C=C2)C=C1)

`REAL300000040680.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040680.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040680/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040680 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC(=O)CC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 14, 15, 14, 38, 39, 38, 39, 1, 1, 3, 3, 3, 3, 1, 1, 6, 14, 38, 38, 1, 1, 3, 3] 42
rigid atoms, others: [34, 33, 6, 7, 8, 9, 10, 11, 21, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 29, 30, 31, 32, 35, 36])
total number of confs: 152
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040680 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC(=O)CC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 1, 3, 9, 9, 17, 17, 17, 42, 42, 42, 42, 3, 3, 1, 1, 1, 1, 3, 3, 9, 17, 42, 42, 3, 3, 1, 1] 42
rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 23, 24, 25, 26, 36] 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: 162
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040680 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040680
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040680/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040680
Building REAL300000040681
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040681'
/scratch/stefan/7769621/working/building/REAL300000040681 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040681

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040681/0 /scratch/stefan/7769621/working/building/REAL300000040681 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 780)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/780
`/scratch/stefan/7769621/working/3D/780' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2NC=C(C=NNC(=O)CC(F)(F)F)C2=C1)

`REAL300000040681.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040681.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040681/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040681 none O=C([O-])C1=CC=C2NC=C(C=NNC(=O)CC(F)(F)F)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 4, 6, 29, 29, 1] 29
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29])
total number of confs: 99
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040681 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040681
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040681/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040681
Building REAL300000040682
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040682'
/scratch/stefan/7769621/working/building/REAL300000040682 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040682

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040682/0 /scratch/stefan/7769621/working/building/REAL300000040682 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 781)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/781
`/scratch/stefan/7769621/working/3D/781' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)CC(F)(F)F)=CC(Cl)=C1OC(C)C(=O)[O-])

`REAL300000040682.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040682.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040682/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040682 none COC1=CC(C=NNC(=O)CC(F)(F)F)=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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 16, 1, 12, 5, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 8, 8, 20, 20, 20, 81, 81, 81, 81, 1, 1, 1, 1, 1, 4, 12, 12, 20, 20, 4, 4, 4, 1, 8, 20, 81, 81, 1, 12, 13, 13, 13] 201
rigid atoms, others: [1, 2, 3, 4, 5, 33, 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, 34, 35, 36, 37])
total number of confs: 366
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040682 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040682
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040682/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040682
Building REAL300000040683
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040683'
/scratch/stefan/7769621/working/building/REAL300000040683 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040683

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040683/0 /scratch/stefan/7769621/working/building/REAL300000040683 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 782)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/782
`/scratch/stefan/7769621/working/3D/782' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Cl)SC(C=NNC(=O)CC(F)(F)F)=C1)

`REAL300000040683.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040683.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040683/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040683 none O=C([O-])C1=C(Cl)SC(C=NNC(=O)CC(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 10, 22, 22, 22, 94, 94, 94, 94, 1, 10, 22, 94, 94, 1] 95
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 23] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22])
total number of confs: 327
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040683 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040683
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040683/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040683
Building REAL300000040684
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040684'
/scratch/stefan/7769621/working/building/REAL300000040684 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040684

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040684/0 /scratch/stefan/7769621/working/building/REAL300000040684 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 783)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/783
`/scratch/stefan/7769621/working/3D/783' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)CC(F)(F)F)C1=CC=C(C(=O)[O-])C=C1C)

`REAL300000040684.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040684.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040684/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040684 none CC(=NNC(=O)CC(F)(F)F)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 23, 23, 23, 51, 51, 51, 51, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 23, 51, 51, 1, 1, 1, 2, 2, 2] 51
rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 197
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040684 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040684
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040684/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040684
Building REAL300000040685
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040685'
/scratch/stefan/7769621/working/building/REAL300000040685 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040685

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040685/0 /scratch/stefan/7769621/working/building/REAL300000040685 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 784)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/784
`/scratch/stefan/7769621/working/3D/784' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C(Cl)C=C1C=NNC(=O)CC(F)(F)F)

`REAL300000040685.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040685.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040685/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040685 none O=C([O-])C1=CN=C(Cl)C=C1C=NNC(=O)CC(F)(F)F NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 16, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 8, 29, 29, 29, 29, 1, 1, 6, 8, 29, 29] 29
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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/7769621/working/building/REAL300000040685 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040685
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040685/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040685
Building REAL300000040686
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040686'
/scratch/stefan/7769621/working/building/REAL300000040686 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040686

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040686/0 /scratch/stefan/7769621/working/building/REAL300000040686 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 785)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/785
`/scratch/stefan/7769621/working/3D/785' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C2=CC=C(C=NNC(=O)CC(F)(F)F)O2)=CC=C1O)

`REAL300000040686.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040686.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040686/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040686 none O=C([O-])C1=CC(C2=CC=C(C=NNC(=O)CC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 8, 1, 11, 5, 5, 15, 15, 15, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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: [25, 13, 25, 13, 13, 1, 1, 1, 1, 1, 1, 4, 4, 18, 18, 18, 78, 78, 78, 78, 1, 13, 13, 12, 12, 13, 1, 1, 4, 18, 78, 78, 13, 13, 26] 402
rigid atoms, others: [5, 6, 7, 8, 9, 10, 20, 26, 27] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 354
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040686 none O=C([O-])C1=CC(C2=CC=C(C=NNC(=O)CC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 8, 1, 11, 5, 5, 15, 15, 15, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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, 39, 39, 81, 81, 77, 201, 201, 201, 201, 13, 1, 1, 1, 1, 1, 13, 13, 39, 81, 201, 201, 1, 1, 2] 402
rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 21, 22, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 34])
total number of confs: 741
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040686 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040686
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040686/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040686
Building REAL300000040687
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040687'
/scratch/stefan/7769621/working/building/REAL300000040687 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040687

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040687/0 /scratch/stefan/7769621/working/building/REAL300000040687 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 786)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/786
`/scratch/stefan/7769621/working/3D/786' -> `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=NNC(=O)CC(F)(F)F)

`REAL300000040687.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040687.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040687/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040687 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC(=O)CC(F)(F)F 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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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, 1, 11, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 11, 11, 22, 22, 22, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 1, 1, 1, 11, 22, 48, 48] 49
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])
total number of confs: 187
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040687 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040687
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040687/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040687
Building REAL300000040688
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040688'
/scratch/stefan/7769621/working/building/REAL300000040688 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040688

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040688/0 /scratch/stefan/7769621/working/building/REAL300000040688 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 787)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/787
`/scratch/stefan/7769621/working/3D/787' -> `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=NNC(=O)CC(F)(F)F)S2)C=C1)

`REAL300000040688.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040688.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040688/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040688 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC(=O)CC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'C.ar', '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, 8, 1, 11, 5, 5, 15, 15, 15, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 9, 9, 27, 27, 27, 74, 74, 74, 74, 1, 7, 7, 7, 7, 1, 1, 9, 27, 74, 74, 7, 7] 118
rigid atoms, others: [6, 7, 8, 9, 10, 11, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 304
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040688 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC(=O)CC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'C.ar', '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, 8, 1, 11, 5, 5, 15, 15, 15, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 9, 9, 9, 35, 35, 67, 67, 67, 118, 118, 118, 118, 9, 1, 1, 1, 1, 9, 9, 35, 67, 118, 118, 1, 1] 118
rigid atoms, others: [32, 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])
total number of confs: 412
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040688 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040688
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040688/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040688
Building REAL300000040689
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040689'
/scratch/stefan/7769621/working/building/REAL300000040689 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040689

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040689/0 /scratch/stefan/7769621/working/building/REAL300000040689 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 788)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/788
`/scratch/stefan/7769621/working/3D/788' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C2=CC=C(C=NNC(=O)CC(F)(F)F)S2)=CC=C1)

`REAL300000040689.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040689.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040689/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040689 none O=C([O-])C1=CC(C2=CC=C(C=NNC(=O)CC(F)(F)F)S2)=CC=C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 5, 5, 15, 15, 15, 14, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 12, 12, 1, 1, 1, 1, 1, 1, 11, 11, 28, 28, 28, 100, 100, 100, 100, 1, 12, 12, 12, 12, 1, 1, 11, 28, 100, 100, 12, 12, 12] 201
rigid atoms, others: [5, 6, 7, 8, 9, 10, 20, 25, 26] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 347
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040689 none O=C([O-])C1=CC(C2=CC=C(C=NNC(=O)CC(F)(F)F)S2)=CC=C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 5, 5, 15, 15, 15, 14, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 12, 12, 12, 12, 48, 48, 102, 102, 102, 201, 201, 201, 201, 12, 1, 1, 1, 1, 12, 12, 48, 102, 201, 201, 1, 1, 1] 201
rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 21, 22, 23, 24, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30])
total number of confs: 740
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040689 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040689
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040689/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040689
Building REAL300000040690
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040690'
/scratch/stefan/7769621/working/building/REAL300000040690 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040690

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040690/0 /scratch/stefan/7769621/working/building/REAL300000040690 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 789)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/789
`/scratch/stefan/7769621/working/3D/789' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC(C(=O)[O-])=C(C=NNC(=O)CC(F)(F)F)S1)

`REAL300000040690.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040690.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040690/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040690 none CCC1=CC(C(=O)[O-])=C(C=NNC(=O)CC(F)(F)F)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 1, 1, 1, 1, 3, 3, 1, 1, 5, 5, 11, 11, 11, 46, 46, 46, 46, 1, 9, 9, 9, 8, 8, 1, 5, 11, 46, 46] 72
rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 19, 25] set([0, 6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 26, 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/7769621/working/building/REAL300000040690 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040690
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040690/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040690
Building REAL300000040691
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040691'
/scratch/stefan/7769621/working/building/REAL300000040691 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040691

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040691/0 /scratch/stefan/7769621/working/building/REAL300000040691 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 790)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/790
`/scratch/stefan/7769621/working/3D/790' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=NNC(=O)CC(F)(F)F)

`REAL300000040691.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040691.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040691/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040691 none COC1=CC=C(C(=O)[O-])C=C1C=NNC(=O)CC(F)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 1, 12, 12, 50, 50, 50, 141, 141, 141, 141, 3, 3, 3, 1, 1, 1, 12, 50, 141, 141] 142
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30])
total number of confs: 491
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040691 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040691
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040691/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040691
Building REAL300000040692
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040692'
/scratch/stefan/7769621/working/building/REAL300000040692 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040692

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040692/0 /scratch/stefan/7769621/working/building/REAL300000040692 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 791)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/791
`/scratch/stefan/7769621/working/3D/791' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2SC=C(C=NNC(=O)CC(F)(F)F)C2=C1)

`REAL300000040692.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040692.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040692/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040692 none O=C([O-])C1=CC=C2SC=C(C=NNC(=O)CC(F)(F)F)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 1, 1, 1, 4, 4, 6, 6, 6, 29, 29, 29, 29, 1, 1, 1, 1, 1, 4, 6, 29, 29, 1] 29
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 29] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28])
total number of confs: 103
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040692 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040692
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040692/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040692
Building REAL300000040693
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040693'
/scratch/stefan/7769621/working/building/REAL300000040693 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040693

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040693/0 /scratch/stefan/7769621/working/building/REAL300000040693 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 792)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/792
`/scratch/stefan/7769621/working/3D/792' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2CCCC(=NNC(=O)CC(F)(F)F)C2=C1)

`REAL300000040693.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040693.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040693/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040693 none O=C([O-])C1=CN=C2CCCC(=NNC(=O)CC(F)(F)F)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 20, 20, 1] 20
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31])
total number of confs: 71
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040693 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040693
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040693/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040693
Building REAL300000040694
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040694'
/scratch/stefan/7769621/working/building/REAL300000040694 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040694

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040694/0 /scratch/stefan/7769621/working/building/REAL300000040694 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 793)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/793
`/scratch/stefan/7769621/working/3D/793' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(Br)C(C=NNC(=O)CC(F)(F)F)=C1)

`REAL300000040694.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040694.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040694/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040694 none O=C([O-])C1=CC=C(Br)C(C=NNC(=O)CC(F)(F)F)=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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 11, 11, 36, 36, 36, 73, 73, 73, 73, 1, 1, 1, 11, 36, 73, 73, 1] 73
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 26] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25])
total number of confs: 265
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040694 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040694
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040694/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040694
Building REAL300000040695
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040695'
/scratch/stefan/7769621/working/building/REAL300000040695 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040695

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040695/0 /scratch/stefan/7769621/working/building/REAL300000040695 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 794)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/794
`/scratch/stefan/7769621/working/3D/794' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)CC(F)(F)F)=CC=C1C(=O)[O-])

`REAL300000040695.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040695.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040695/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040695 none COC1=CC(C=NNC(=O)CC(F)(F)F)=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
163  conformations in input
total number of sets (complete confs): 163
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 11, 11, 34, 34, 34, 143, 143, 143, 143, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 11, 34, 143, 143, 1, 1] 163
rigid atoms, others: [1, 2, 3, 4, 5, 15, 16, 17, 18, 24, 29, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 25, 26, 27, 28])
total number of confs: 495
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040695 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040695
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040695/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040695
Building REAL300000040696
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040696'
/scratch/stefan/7769621/working/building/REAL300000040696 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040696

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040696/0 /scratch/stefan/7769621/working/building/REAL300000040696 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 795)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/795
`/scratch/stefan/7769621/working/3D/795' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(F)=C(C=NNC(=O)CC(F)(F)F)C(F)=C1)

`REAL300000040696.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040696.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040696/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040696 none O=C([O-])C1=CC(F)=C(C=NNC(=O)CC(F)(F)F)C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 15, 1, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 14, 15, 14, 31, 31, 31, 31, 1, 1, 1, 1, 9, 14, 30, 30, 1] 31
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 26] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25])
total number of confs: 121
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040696 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040696
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040696/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040696
Building REAL300000040697
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040697'
/scratch/stefan/7769621/working/building/REAL300000040697 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040697

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040697/0 /scratch/stefan/7769621/working/building/REAL300000040697 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 796)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/796
`/scratch/stefan/7769621/working/3D/796' -> `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=NNC(=O)CC(F)(F)F)=C1)

`REAL300000040697.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040697.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040697/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040697 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC(=O)CC(F)(F)F)=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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 7, 6, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 31, 31, 31, 60, 60, 60, 60, 1, 1, 2, 12, 31, 60, 60, 1] 120
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26])
total number of confs: 220
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040697 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040697/1 /scratch/stefan/7769621/working/building/REAL300000040697 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 797)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/797
`/scratch/stefan/7769621/working/3D/797' -> `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=NNC(=O)CC(F)(F)F)=C1)

`REAL300000040697.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040697.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040697/1/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: REAL300000040697 none O=C([O-])C1=CC(Br)=C([O-])C(C=NNC(=O)CC(F)(F)F)=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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 18, 18, 18, 18, 1, 1, 6, 10, 18, 18, 1] 18
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25])
total number of confs: 66
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040697 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040697
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040697/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040697/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040697
Building REAL300000040698
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040698'
/scratch/stefan/7769621/working/building/REAL300000040698 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040698

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040698/0 /scratch/stefan/7769621/working/building/REAL300000040698 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 798)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/798
`/scratch/stefan/7769621/working/3D/798' -> `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=NNC(=O)CC(F)(F)F)C=C2)O1)

`REAL300000040698.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040698.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040698/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040698 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC(=O)CC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.3', '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, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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: [25, 24, 25, 24, 24, 24, 9, 2, 1, 1, 1, 1, 1, 1, 11, 11, 33, 33, 33, 104, 104, 104, 104, 1, 1, 24, 24, 24, 9, 9, 1, 1, 11, 33, 104, 104, 1, 1] 201
rigid atoms, others: [36, 37, 8, 9, 10, 11, 12, 13, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35])
total number of confs: 411
number of broken/clashed sets: 40
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040698 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC(=O)CC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.3', '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, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 8, 22, 24, 24, 24, 24, 72, 72, 111, 111, 111, 201, 201, 201, 201, 24, 24, 1, 1, 1, 8, 8, 24, 24, 72, 111, 201, 201, 24, 24] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 722
number of broken/clashed sets: 40
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040698 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040698
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040698/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040698
Building REAL300000040699
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040699'
/scratch/stefan/7769621/working/building/REAL300000040699 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040699

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040699/0 /scratch/stefan/7769621/working/building/REAL300000040699 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 799)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/799
`/scratch/stefan/7769621/working/3D/799' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC=CC=C2C(C=NNC(=O)CC(F)(F)F)=C1O)

`REAL300000040699.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040699.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040699/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040699 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC(=O)CC(F)(F)F)=C1O 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.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', '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, 8, 1, 11, 5, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 22, 22, 22, 68, 68, 68, 68, 1, 1, 1, 1, 1, 1, 1, 10, 22, 68, 68, 2] 136
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28] set([0, 32, 2, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31])
total number of confs: 250
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040699 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040699
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040699/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040699
Building REAL300000040700
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040700'
/scratch/stefan/7769621/working/building/REAL300000040700 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040700

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040700/0 /scratch/stefan/7769621/working/building/REAL300000040700 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 800)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/800
`/scratch/stefan/7769621/working/3D/800' -> `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=NNC(=O)CC(F)(F)F)C=C2)=C1)

`REAL300000040700.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040700.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040700/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040700 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC(=O)CC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 5, 13, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 12, 12, 28, 29, 29, 77, 77, 77, 77, 1, 1, 3, 5, 5, 3, 3, 3, 1, 1, 12, 28, 76, 76, 1, 1, 3] 201
rigid atoms, others: [32, 37, 38, 8, 9, 10, 11, 12, 13, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 39])
total number of confs: 304
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040700 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC(=O)CC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 21, 21, 45, 45, 45, 121, 121, 121, 121, 3, 3, 1, 2, 2, 1, 1, 1, 3, 3, 21, 45, 121, 121, 3, 3, 1] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 39, 25, 28, 29, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 460
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040700 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040700
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040700/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040700
Building REAL300000040701
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040701'
/scratch/stefan/7769621/working/building/REAL300000040701 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040701

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040701/0 /scratch/stefan/7769621/working/building/REAL300000040701 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 801)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/801
`/scratch/stefan/7769621/working/3D/801' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NNC(=O)CC(F)(F)F)SC(Cl)=C1)

`REAL300000040701.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040701.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040701/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040701 none O=C([O-])C1=C(C=NNC(=O)CC(F)(F)F)SC(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 14, 1, 16, 1, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 5, 5, 8, 8, 8, 28, 28, 28, 28, 1, 1, 1, 1, 5, 8, 28, 28, 1] 29
rigid atoms, others: [1, 3, 4, 5, 15, 16, 17, 18, 23] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22])
total number of confs: 108
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040701 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040701
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040701/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040701
Building REAL300000040702
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040702'
/scratch/stefan/7769621/working/building/REAL300000040702 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040702

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040702/0 /scratch/stefan/7769621/working/building/REAL300000040702 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 802)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/802
`/scratch/stefan/7769621/working/3D/802' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC(C=NNC(=O)CC(F)(F)F)=CC=C1OCC(=O)[O-])

`REAL300000040702.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040702.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040702/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040702 none CCOC1=CC(C=NNC(=O)CC(F)(F)F)=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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 12, 5, 1, 11, 11, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 9, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 29, 29, 29, 29, 1, 1, 1, 1, 9, 40, 65, 65, 21, 21, 21, 21, 21, 1, 6, 6, 29, 29, 1, 1, 40, 40] 201
rigid atoms, others: [19, 2, 3, 4, 5, 6, 34, 16, 17, 18, 35, 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, 36, 37])
total number of confs: 373
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040702 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040702
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040702/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040702
Building REAL300000040703
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040703'
/scratch/stefan/7769621/working/building/REAL300000040703 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040703

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040703/0 /scratch/stefan/7769621/working/building/REAL300000040703 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 803)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/803
`/scratch/stefan/7769621/working/3D/803' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC(=O)CC(F)(F)F)

`REAL300000040703.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040703.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040703/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040703 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC(=O)CC(F)(F)F 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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, 8, 1, 11, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [19, 13, 19, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 27, 27, 35, 35, 35, 97, 97, 97, 97, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 27, 35, 97, 97] 97
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37])
total number of confs: 324
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040703 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC(=O)CC(F)(F)F 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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, 8, 1, 11, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
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, 6, 6, 14, 14, 14, 35, 35, 35, 35, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 6, 14, 35, 35] 97
rigid atoms, others: [1, 3, 4, 5, 6, 33, 12, 13, 14] set([0, 2, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 143
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040703 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040703
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040703/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040703
Building REAL300000040704
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040704'
/scratch/stefan/7769621/working/building/REAL300000040704 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040704

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040704/0 /scratch/stefan/7769621/working/building/REAL300000040704 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 804)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/804
`/scratch/stefan/7769621/working/3D/804' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C)C(C=NNC(=O)CC(F)(F)F)=C1C(=O)[O-])

`REAL300000040704.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040704.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040704/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040704 none COC1=CC=C(C)C(C=NNC(=O)CC(F)(F)F)=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.am', 'C.2', 'O.2', 'C.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, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 61, 61, 61, 61, 1, 1, 3, 3, 4, 4, 4, 1, 1, 2, 2, 2, 5, 15, 61, 61] 85
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])
total number of confs: 223
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040704 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040704
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040704/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040704
Building REAL300000040705
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040705'
/scratch/stefan/7769621/working/building/REAL300000040705 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040705

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040705/0 /scratch/stefan/7769621/working/building/REAL300000040705 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 805)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/805
`/scratch/stefan/7769621/working/3D/805' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C2=CC=C(F)C=C2C(C=NNC(=O)CC(F)(F)F)=C1C(=O)[O-])

`REAL300000040705.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040705.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040705/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040705 none CN1C2=CC=C(F)C=C2C(C=NNC(=O)CC(F)(F)F)=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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 1, 11, 5, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 23, 23, 23, 23, 1, 1, 3, 3, 2, 2, 2, 1, 1, 1, 6, 10, 23, 23] 23
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 27, 28, 29] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 87
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040705 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040705
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040705/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040705
Building REAL300000040706
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040706'
/scratch/stefan/7769621/working/building/REAL300000040706 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040706

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040706/0 /scratch/stefan/7769621/working/building/REAL300000040706 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 806)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/806
`/scratch/stefan/7769621/working/3D/806' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)CC(F)(F)F)C1=C(C(=O)[O-])C2=CC=CC=C2S1)

`REAL300000040706.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040706.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040706/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040706 none CC(=NNC(=O)CC(F)(F)F)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 1, 7, 7, 13, 13, 13, 57, 57, 57, 57, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 13, 57, 57, 1, 1, 1, 1] 57
rigid atoms, others: [32, 1, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 23, 24, 25, 26, 27, 28])
total number of confs: 203
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040706 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040706
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040706/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040706
Building REAL300000040707
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040707'
/scratch/stefan/7769621/working/building/REAL300000040707 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040707

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040707/0 /scratch/stefan/7769621/working/building/REAL300000040707 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 807)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/807
`/scratch/stefan/7769621/working/3D/807' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NNC(=O)CC(F)(F)F)SC(Br)=C1)

`REAL300000040707.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040707.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040707/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040707 none O=C([O-])C1=C(C=NNC(=O)CC(F)(F)F)SC(Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 14, 1, 17, 1, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 5, 5, 8, 8, 8, 28, 28, 28, 28, 1, 1, 1, 1, 5, 8, 28, 28, 1] 29
rigid atoms, others: [1, 3, 4, 5, 15, 16, 17, 18, 23] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22])
total number of confs: 108
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040707 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040707
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040707/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040707
Building REAL300000040708
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040708'
/scratch/stefan/7769621/working/building/REAL300000040708 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040708

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040708/0 /scratch/stefan/7769621/working/building/REAL300000040708 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 808)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/808
`/scratch/stefan/7769621/working/3D/808' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C2NC=C(C=NNC(=O)CC(F)(F)F)C2=CC=C1)

`REAL300000040708.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040708.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040708/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040708 none O=C([O-])C1=C2NC=C(C=NNC(=O)CC(F)(F)F)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 10, 18, 19, 18, 57, 57, 57, 57, 1, 1, 1, 1, 1, 1, 10, 18, 56, 56, 1, 1, 1] 57
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 28, 29, 30] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27])
total number of confs: 194
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040708 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040708
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040708/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040708
Building REAL300000040709
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040709'
/scratch/stefan/7769621/working/building/REAL300000040709 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040709

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040709/0 /scratch/stefan/7769621/working/building/REAL300000040709 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 809)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/809
`/scratch/stefan/7769621/working/3D/809' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)CC(F)(F)F)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1)

`REAL300000040709.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040709.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040709/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040709 none CC(=NNC(=O)CC(F)(F)F)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 5, 11, 11, 11, 27, 27, 27, 27, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 27, 27, 1, 1, 1, 1, 1] 27
rigid atoms, others: [32, 1, 34, 33, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 24, 25, 26, 27, 28, 29])
total number of confs: 107
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040709 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040709
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040709/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040709
Building REAL300000040710
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040710'
/scratch/stefan/7769621/working/building/REAL300000040710 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040710

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040710/0 /scratch/stefan/7769621/working/building/REAL300000040710 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 810)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/810
`/scratch/stefan/7769621/working/3D/810' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC(C=NNC(=O)CC(F)(F)F)=CC=C2O1)

`REAL300000040710.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040710.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040710/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040710 none O=C([O-])C1=CC2=CC(C=NNC(=O)CC(F)(F)F)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 1, 7, 7, 17, 17, 17, 42, 42, 42, 42, 1, 1, 1, 1, 1, 1, 7, 17, 42, 42, 1, 1] 43
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 28, 29] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27])
total number of confs: 156
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040710 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040710
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040710/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040710
Building REAL300000040711
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040711'
/scratch/stefan/7769621/working/building/REAL300000040711 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040711

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040711/0 /scratch/stefan/7769621/working/building/REAL300000040711 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 811)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/811
`/scratch/stefan/7769621/working/3D/811' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2C(C=NNC(=O)CC(F)(F)F)=CC=CN12)

`REAL300000040711.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040711.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040711/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040711 none O=C([O-])C1=CN=C2C(C=NNC(=O)CC(F)(F)F)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9, 23, 23, 23, 23, 1, 1, 1, 1, 1, 3, 9, 23, 23, 1, 1, 1] 24
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 27, 28, 29] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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/7769621/working/building/REAL300000040711 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040711
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040711/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040711
Building REAL300000040712
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040712'
/scratch/stefan/7769621/working/building/REAL300000040712 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040712

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040712/0 /scratch/stefan/7769621/working/building/REAL300000040712 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 812)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/812
`/scratch/stefan/7769621/working/3D/812' -> `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=NNC(=O)CC(F)(F)F)O1)

`REAL300000040712.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040712.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040712/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040712 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC(=O)CC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'O.3', '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, 8, 1, 11, 5, 5, 15, 15, 15, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [71, 71, 71, 71, 71, 71, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 24, 24, 24, 24, 71, 71, 71, 21, 21, 1, 1, 1, 1, 4, 4, 24, 24] 201
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, 35, 36, 37])
total number of confs: 211
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040712 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC(=O)CC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'O.3', '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, 8, 1, 11, 5, 5, 15, 15, 15, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 27, 71, 71, 71, 71, 71, 71, 94, 94, 94, 94, 94, 201, 201, 201, 201, 1, 1, 1, 7, 7, 71, 71, 71, 71, 94, 94, 201, 201] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 661
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040712 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040712
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040712/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040712
Building REAL300000040713
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040713'
/scratch/stefan/7769621/working/building/REAL300000040713 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040713

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040713/0 /scratch/stefan/7769621/working/building/REAL300000040713 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 813)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/813
`/scratch/stefan/7769621/working/3D/813' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Br)C=CC=C1C=NNC(=O)CC(F)(F)F)

`REAL300000040713.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040713.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040713/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040713 none O=C([O-])C1=C(Br)C=CC=C1C=NNC(=O)CC(F)(F)F 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 1, 1, 1, 6, 6, 6, 6, 6, 17, 17, 17, 17, 1, 1, 1, 6, 6, 17, 17] 17
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26])
total number of confs: 59
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040713 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040713
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040713/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040713
Building REAL300000040714
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040714'
/scratch/stefan/7769621/working/building/REAL300000040714 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040714

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040714/0 /scratch/stefan/7769621/working/building/REAL300000040714 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 814)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/814
`/scratch/stefan/7769621/working/3D/814' -> `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=NNC(=O)CC(F)(F)F)

`REAL300000040714.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040714.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040714/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040714 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NNC(=O)CC(F)(F)F 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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, 8, 1, 11, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 8, 8, 16, 16, 16, 96, 96, 96, 96, 3, 3, 3, 1, 4, 4, 4, 1, 1, 8, 16, 96, 96] 100
rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 34, 15, 16, 33, 29] set([0, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 35, 36, 37, 38])
total number of confs: 349
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040714 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040714
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040714/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040714
Building REAL300000040715
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040715'
/scratch/stefan/7769621/working/building/REAL300000040715 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040715

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040715/0 /scratch/stefan/7769621/working/building/REAL300000040715 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 815)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/815
`/scratch/stefan/7769621/working/3D/815' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NNC(=O)CC(F)(F)F)C2=C(C=C1)OCO2)

`REAL300000040715.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040715.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040715/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040715 none O=C([O-])C1=C(C=NNC(=O)CC(F)(F)F)C2=C(C=C1)OCO2 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 1, 1, 12, 5, 12, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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, 1, 1, 1, 7, 7, 10, 10, 10, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 1, 7, 10, 33, 33, 1, 1, 1, 1] 33
rigid atoms, others: [1, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25])
total number of confs: 120
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040715 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040715
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040715/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040715
Building REAL300000040716
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040716'
/scratch/stefan/7769621/working/building/REAL300000040716 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040716

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040716/0 /scratch/stefan/7769621/working/building/REAL300000040716 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 816)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/816
`/scratch/stefan/7769621/working/3D/816' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC(=O)CC(F)(F)F)C=C1Cl)

`REAL300000040716.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040716.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040716/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040716 none O=C([O-])COC1=CC=C(C=NNC(=O)CC(F)(F)F)C=C1Cl 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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 11, 5, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 37, 56, 10, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 63, 63, 63, 63, 1, 1, 1, 37, 37, 1, 1, 6, 17, 63, 63, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 19, 20, 21, 24, 25, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27, 28, 29])
total number of confs: 388
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040716 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040716
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040716/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040716
Building REAL300000040717
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040717'
/scratch/stefan/7769621/working/building/REAL300000040717 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040717

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040717/0 /scratch/stefan/7769621/working/building/REAL300000040717 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 817)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/817
`/scratch/stefan/7769621/working/3D/817' -> `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=NNC(=O)CC(F)(F)F)C=C1)

`REAL300000040717.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040717.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040717/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040717 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC(=O)CC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9, 33, 33, 33, 33, 1, 1, 9, 9, 5, 1, 1, 6, 8, 33, 33, 1, 1] 63
rigid atoms, others: [33, 34, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 27, 28] set([0, 1, 2, 3, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31])
total number of confs: 153
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040717 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040717
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040717/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040717
Building REAL300000040718
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040718'
/scratch/stefan/7769621/working/building/REAL300000040718 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040718

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040718/0 /scratch/stefan/7769621/working/building/REAL300000040718 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 818)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/818
`/scratch/stefan/7769621/working/3D/818' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=C(C=NNC(=O)CC(F)(F)F)C(F)=CC=C2S1)

`REAL300000040718.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040718.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040718/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040718 none O=C([O-])C1=CC2=C(C=NNC(=O)CC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 11, 11, 21, 21, 21, 54, 54, 54, 54, 1, 1, 1, 1, 1, 1, 1, 11, 21, 54, 54, 1, 1] 54
rigid atoms, others: [1, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27])
total number of confs: 210
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040718 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040718
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040718/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040718
Building REAL300000040719
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040719'
/scratch/stefan/7769621/working/building/REAL300000040719 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040719

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040719/0 /scratch/stefan/7769621/working/building/REAL300000040719 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 819)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/819
`/scratch/stefan/7769621/working/3D/819' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=NNC(=O)CC(F)(F)F)

`REAL300000040719.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040719.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040719/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040719 none COC1=CC(C(=O)[O-])=CC=C1C=NNC(=O)CC(F)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 10, 10, 18, 18, 18, 52, 52, 52, 52, 3, 3, 3, 1, 1, 1, 10, 18, 52, 52] 52
rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 11, 24, 25, 26] set([0, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30])
total number of confs: 191
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040719 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040719
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040719/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040719
Building REAL300000040720
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040720'
/scratch/stefan/7769621/working/building/REAL300000040720 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040720

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040720/0 /scratch/stefan/7769621/working/building/REAL300000040720 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 820)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/820
`/scratch/stefan/7769621/working/3D/820' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC(=O)CC(F)(F)F)=N2)C1)

`REAL300000040720.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040720.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040720/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040720 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC(=O)CC(F)(F)F)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 13, 25, 13, 13, 13, 1, 13, 1, 1, 1, 1, 1, 6, 6, 16, 16, 16, 75, 75, 75, 75, 1, 13, 13, 13, 1, 1, 6, 16, 75, 75, 13, 13] 201
rigid atoms, others: [6, 8, 9, 10, 11, 12, 22, 26, 27] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 320
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040720 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC(=O)CC(F)(F)F)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 15, 15, 15, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 13, 13, 13, 13, 38, 38, 78, 78, 78, 201, 201, 201, 201, 13, 1, 1, 1, 13, 13, 38, 78, 201, 201, 1, 1] 201
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 23, 24, 25, 33] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31])
total number of confs: 715
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040720 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040720
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040720/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040720
Building REAL300000040721
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040721'
/scratch/stefan/7769621/working/building/REAL300000040721 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040721

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040721/0 /scratch/stefan/7769621/working/building/REAL300000040721 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 821)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/821
`/scratch/stefan/7769621/working/3D/821' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=CC=C1C=NNC(=O)NCC(F)(F)F)

`REAL300000040721.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040721.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040721/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040721 none O=C([O-])COC1=CC=CC=C1C=NNC(=O)NCC(F)(F)F 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.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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, 11, 8, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [75, 50, 75, 10, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 12, 12, 56, 56, 56, 56, 50, 50, 1, 1, 1, 1, 4, 12, 12, 56, 56] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27] set([0, 1, 2, 3, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31])
total number of confs: 434
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040721 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040721
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040721/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040721
Building REAL300000040722
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040722'
/scratch/stefan/7769621/working/building/REAL300000040722 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040722

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040722/0 /scratch/stefan/7769621/working/building/REAL300000040722 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 822)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/822
`/scratch/stefan/7769621/working/3D/822' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NCC(F)(F)F)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1)

`REAL300000040722.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040722.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040722/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040722 none CC(=NNC(=O)NCC(F)(F)F)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.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 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
153  conformations in input
total number of sets (complete confs): 153
using faster count positions algorithm for large data
unique positions, atoms: [17, 1, 16, 27, 103, 103, 114, 115, 153, 153, 153, 153, 1, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 18, 27, 27, 102, 115, 153, 153, 13, 13, 1, 1, 13, 13] 153
rigid atoms, others: [35, 36, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 555
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040722 none CC(=NNC(=O)NCC(F)(F)F)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.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 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
153  conformations in input
total number of sets (complete confs): 153
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 32, 32, 32, 32, 106, 106, 106, 106, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 1, 1, 6, 6, 6, 32, 32, 106, 106, 1, 1, 13, 13, 1, 1] 153
rigid atoms, others: [1, 34, 37, 38, 33, 12, 13, 14, 15, 16, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 382
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040722 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040722
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040722/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040722
Building REAL300000040723
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040723'
/scratch/stefan/7769621/working/building/REAL300000040723 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040723

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040723/0 /scratch/stefan/7769621/working/building/REAL300000040723 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 823)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/823
`/scratch/stefan/7769621/working/3D/823' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)NCC(F)(F)F)=CC=C1OCC(=O)[O-])

`REAL300000040723.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040723.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040723/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040723 none COC1=CC(C=NNC(=O)NCC(F)(F)F)=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.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 9, 9, 9, 39, 39, 39, 39, 1, 1, 1, 1, 9, 38, 60, 60, 3, 3, 3, 1, 7, 9, 9, 39, 39, 1, 1, 38, 38] 201
rigid atoms, others: [1, 2, 3, 4, 5, 33, 34, 16, 17, 18, 19, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 330
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040723 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040723
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040723/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040723
Building REAL300000040724
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040724'
/scratch/stefan/7769621/working/building/REAL300000040724 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040724

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040724/0 /scratch/stefan/7769621/working/building/REAL300000040724 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 824)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/824
`/scratch/stefan/7769621/working/3D/824' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC(=O)NCC(F)(F)F)C=C1)

`REAL300000040724.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040724.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040724/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040724 none O=C([O-])COC1=CC=C(C=NNC(=O)NCC(F)(F)F)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.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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, 11, 8, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 14, 28, 4, 1, 1, 1, 1, 1, 1, 8, 8, 22, 23, 23, 23, 87, 87, 87, 87, 1, 1, 14, 14, 1, 1, 8, 22, 23, 87, 87, 1, 1] 201
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 20, 21, 24, 25, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28, 29, 30])
total number of confs: 387
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040724 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040724
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040724/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040724
Building REAL300000040725
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040725'
/scratch/stefan/7769621/working/building/REAL300000040725 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040725

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040725/0 /scratch/stefan/7769621/working/building/REAL300000040725 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 825)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/825
`/scratch/stefan/7769621/working/3D/825' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NCC(F)(F)F)C1=CC=CC(OCC(=O)[O-])=C1)

`REAL300000040725.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040725.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040725/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040725 none CC(=NNC(=O)NCC(F)(F)F)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 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: [10, 1, 10, 10, 18, 18, 18, 18, 58, 58, 58, 58, 1, 1, 1, 1, 1, 1, 6, 22, 34, 34, 1, 10, 10, 10, 18, 18, 58, 58, 1, 1, 1, 22, 22, 1] 201
rigid atoms, others: [32, 1, 35, 12, 13, 14, 15, 16, 17, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 304
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040725 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040725
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040725/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040725
Building REAL300000040726
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040726'
/scratch/stefan/7769621/working/building/REAL300000040726 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040726

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040726/0 /scratch/stefan/7769621/working/building/REAL300000040726 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 826)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/826
`/scratch/stefan/7769621/working/3D/826' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NCC(F)(F)F)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1)

`REAL300000040726.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040726.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040726/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040726 none CC(=NNC(=O)NCC(F)(F)F)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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]
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, 11, 11, 11, 11, 52, 52, 52, 52, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 17, 1, 1, 6, 6, 6, 11, 11, 52, 52, 1, 1, 9, 17, 17, 1, 1] 156
rigid atoms, others: [1, 34, 38, 33, 39, 12, 13, 14, 15, 16, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37])
total number of confs: 254
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040726 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040726
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040726/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040726
Building REAL300000040727
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040727'
/scratch/stefan/7769621/working/building/REAL300000040727 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040727

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040727/0 /scratch/stefan/7769621/working/building/REAL300000040727 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 827)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/827
`/scratch/stefan/7769621/working/3D/827' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NCC(F)(F)F)C1=CC=C(C(=O)[O-])C=C1)

`REAL300000040727.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040727.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040727/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040727 none CC(=NNC(=O)NCC(F)(F)F)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [4, 1, 4, 4, 16, 16, 16, 16, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 16, 16, 34, 34, 1, 1, 1, 1] 34
rigid atoms, others: [1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 138
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040727 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040727
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040727/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040727
Building REAL300000040728
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040728'
/scratch/stefan/7769621/working/building/REAL300000040728 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040728

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040728/0 /scratch/stefan/7769621/working/building/REAL300000040728 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 828)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/828
`/scratch/stefan/7769621/working/3D/828' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NCC(F)(F)F)C1=CC=C(CC(=O)[O-])C=C1)

`REAL300000040728.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040728.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040728/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040728 none CC(=NNC(=O)NCC(F)(F)F)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 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
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 24, 24, 24, 24, 50, 50, 50, 50, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 6, 6, 6, 24, 24, 50, 50, 1, 1, 3, 3, 1, 1] 72
rigid atoms, others: [1, 34, 33, 12, 13, 14, 15, 16, 20, 21, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32])
total number of confs: 200
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040728 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040728
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040728/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040728
Building REAL300000040729
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040729'
/scratch/stefan/7769621/working/building/REAL300000040729 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040729

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040729/0 /scratch/stefan/7769621/working/building/REAL300000040729 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 829)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/829
`/scratch/stefan/7769621/working/3D/829' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])OC2=C1C(=NNC(=O)NCC(F)(F)F)CCC2)

`REAL300000040729.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040729.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040729/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040729 none CC1=C(C(=O)[O-])OC2=C1C(=NNC(=O)NCC(F)(F)F)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.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 5, 7, 7, 7, 6, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 9, 10, 10, 10, 35, 35, 35, 35, 1, 1, 1, 2, 2, 2, 9, 10, 35, 35, 1, 1, 1, 1, 1, 1] 35
rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 11, 34, 35, 20, 21, 22, 30, 31] set([4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 135
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040729 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040729
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040729/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040729
Building REAL300000040730
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040730'
/scratch/stefan/7769621/working/building/REAL300000040730 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040730

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040730/0 /scratch/stefan/7769621/working/building/REAL300000040730 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 830)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/830
`/scratch/stefan/7769621/working/3D/830' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=C(C=NNC(=O)NCC(F)(F)F)C=C1)

`REAL300000040730.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040730.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040730/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040730 none O=C([O-])CCOC1=CC=C(C=NNC(=O)NCC(F)(F)F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 20, 27, 14, 4, 1, 1, 1, 1, 1, 1, 8, 8, 24, 25, 25, 25, 88, 88, 88, 88, 1, 1, 20, 20, 14, 14, 1, 1, 8, 24, 25, 88, 88, 1, 1] 201
rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 21, 22, 27, 28] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 29, 30, 31, 32, 33])
total number of confs: 422
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040730 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040730
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040730/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040730
Building REAL300000040731
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040731'
/scratch/stefan/7769621/working/building/REAL300000040731 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040731

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040731/0 /scratch/stefan/7769621/working/building/REAL300000040731 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 831)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/831
`/scratch/stefan/7769621/working/3D/831' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(Br)C=C1C=NNC(=O)NCC(F)(F)F)

`REAL300000040731.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040731.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040731/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040731 none O=C([O-])COC1=CC=C(Br)C=C1C=NNC(=O)NCC(F)(F)F 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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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, 8, 1, 11, 8, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [79, 49, 79, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 12, 12, 56, 56, 56, 56, 49, 49, 1, 1, 1, 4, 12, 12, 56, 56] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27] set([0, 1, 2, 3, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31])
total number of confs: 444
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040731 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040731
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040731/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040731
Building REAL300000040732
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040732'
/scratch/stefan/7769621/working/building/REAL300000040732 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040732

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040732/0 /scratch/stefan/7769621/working/building/REAL300000040732 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 832)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/832
`/scratch/stefan/7769621/working/3D/832' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=CC(C=NNC(=O)NCC(F)(F)F)=C1)C(=O)[O-])

`REAL300000040732.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040732.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040732/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040732 none CC(OC1=CC=CC(C=NNC(=O)NCC(F)(F)F)=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.am', 'C.2', 'O.2', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 11, 1, 1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 55, 55, 55, 55, 1, 29, 45, 45, 29, 29, 29, 29, 1, 1, 1, 6, 11, 12, 55, 55, 1] 201
rigid atoms, others: [35, 2, 3, 4, 5, 6, 7, 8, 19, 27, 28, 29] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34])
total number of confs: 342
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040732 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040732
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040732/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040732
Building REAL300000040733
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040733'
/scratch/stefan/7769621/working/building/REAL300000040733 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040733

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040733/0 /scratch/stefan/7769621/working/building/REAL300000040733 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 833)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/833
`/scratch/stefan/7769621/working/3D/833' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=CC(C=NNC(=O)NCC(F)(F)F)=C1)

`REAL300000040733.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040733.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040733/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040733 none O=C([O-])CCOC1=CC=CC(C=NNC(=O)NCC(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [48, 36, 43, 24, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 13, 14, 14, 14, 56, 56, 56, 56, 1, 36, 36, 24, 24, 1, 1, 1, 6, 13, 14, 56, 56, 1] 201
rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11, 22, 27, 28, 29] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 30, 31, 32, 33, 34])
total number of confs: 366
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040733 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040733
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040733/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040733
Building REAL300000040734
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040734'
/scratch/stefan/7769621/working/building/REAL300000040734 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040734

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040734/0 /scratch/stefan/7769621/working/building/REAL300000040734 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 834)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/834
`/scratch/stefan/7769621/working/3D/834' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC=C1COC1=CC(C=NNC(=O)NCC(F)(F)F)=CC=C1)

`REAL300000040734.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040734.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040734/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040734 none O=C([O-])C1=CC=CC=C1COC1=CC(C=NNC(=O)NCC(F)(F)F)=CC=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.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 7, 6, 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
128  conformations in input
total number of sets (complete confs): 128
using faster count positions algorithm for large data
unique positions, atoms: [17, 15, 17, 15, 15, 15, 15, 15, 7, 3, 1, 1, 1, 1, 1, 8, 8, 20, 21, 21, 21, 56, 56, 56, 56, 1, 1, 1, 15, 15, 15, 15, 7, 7, 1, 8, 20, 21, 56, 56, 1, 1, 1] 128
rigid atoms, others: [34, 40, 41, 10, 11, 12, 13, 14, 25, 26, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39])
total number of confs: 246
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040734 none O=C([O-])C1=CC=CC=C1COC1=CC(C=NNC(=O)NCC(F)(F)F)=CC=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.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 7, 6, 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
128  conformations in input
total number of sets (complete confs): 128
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 9, 15, 15, 15, 37, 37, 58, 58, 58, 58, 128, 128, 128, 128, 14, 15, 15, 1, 1, 1, 1, 5, 5, 15, 37, 58, 58, 128, 128, 14, 15, 15] 128
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 2, 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])
total number of confs: 492
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040734 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040734
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040734/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040734
Building REAL300000040735
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040735'
/scratch/stefan/7769621/working/building/REAL300000040735 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040735

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040735/0 /scratch/stefan/7769621/working/building/REAL300000040735 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 835)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/835
`/scratch/stefan/7769621/working/3D/835' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC(=O)NCC(F)(F)F)C=C1[N+](=O)[O-])

`REAL300000040735.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040735.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040735/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040735 none O=C([O-])COC1=CC=C(C=NNC(=O)NCC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 11, 8, 5, 5, 15, 15, 15, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [40, 27, 40, 7, 1, 1, 1, 1, 1, 1, 6, 6, 18, 19, 19, 19, 89, 89, 89, 89, 1, 1, 1, 2, 2, 27, 27, 1, 1, 6, 18, 19, 89, 89, 1] 201
rigid atoms, others: [34, 4, 5, 6, 7, 8, 9, 20, 21, 22, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 29, 30, 31, 32, 33])
total number of confs: 448
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040735 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040735
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040735/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040735
Building REAL300000040736
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040736'
/scratch/stefan/7769621/working/building/REAL300000040736 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040736

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040736/0 /scratch/stefan/7769621/working/building/REAL300000040736 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 836)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/836
`/scratch/stefan/7769621/working/3D/836' -> `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=NNC(=O)NCC(F)(F)F)C=C2)=C1)

`REAL300000040736.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040736.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040736/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040736 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC(=O)NCC(F)(F)F)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.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 13, 21, 21, 13, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 21, 21, 21, 21, 83, 83, 83, 83, 1, 1, 13, 13, 13, 13, 3, 3, 1, 1, 9, 21, 21, 83, 83, 1, 1, 13] 201
rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 14, 40, 41, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 42])
total number of confs: 343
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040736 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC(=O)NCC(F)(F)F)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.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 13, 13, 13, 13, 13, 43, 43, 71, 71, 71, 71, 201, 201, 201, 201, 13, 13, 1, 2, 2, 2, 9, 9, 13, 13, 43, 71, 71, 201, 201, 12, 13, 1] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 42, 27] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 755
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040736 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040736
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040736/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040736
Building REAL300000040737
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040737'
/scratch/stefan/7769621/working/building/REAL300000040737 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040737

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040737/0 /scratch/stefan/7769621/working/building/REAL300000040737 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 837)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/837
`/scratch/stefan/7769621/working/3D/837' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(COC2=CC(C=NNC(=O)NCC(F)(F)F)=CC=C2)=CC=C1)

`REAL300000040737.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040737.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040737/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040737 none O=C([O-])C1=CC(COC2=CC(C=NNC(=O)NCC(F)(F)F)=CC=C2)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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: [11, 1, 11, 1, 1, 1, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 19, 19, 19, 5, 3, 1, 1, 1, 1, 1, 8, 8, 14, 15, 15, 15, 39, 39, 39, 39, 1, 1, 1, 19, 19, 19, 19, 5, 5, 1, 8, 14, 15, 39, 39, 1, 1, 1, 19, 19, 19] 201
rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 22, 23, 24, 39, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 40, 41, 42])
total number of confs: 165
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040737 none O=C([O-])C1=CC(COC2=CC(C=NNC(=O)NCC(F)(F)F)=CC=C2)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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: [11, 1, 11, 1, 1, 1, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 10, 19, 19, 19, 71, 71, 97, 97, 97, 97, 201, 201, 201, 201, 18, 19, 19, 1, 1, 1, 1, 8, 8, 19, 71, 97, 97, 201, 201, 18, 19, 19, 1, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 40, 41, 42, 25, 26, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 786
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040737 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040737
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040737/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040737
Building REAL300000040738
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040738'
/scratch/stefan/7769621/working/building/REAL300000040738 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040738

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040738/0 /scratch/stefan/7769621/working/building/REAL300000040738 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 838)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/838
`/scratch/stefan/7769621/working/3D/838' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=CC(C=NNC(=O)NCC(F)(F)F)=C1)

`REAL300000040738.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040738.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040738/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040738 none O=C([O-])COC1=CC=CC(C=NNC(=O)NCC(F)(F)F)=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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [43, 27, 43, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 14, 15, 15, 15, 57, 57, 57, 57, 1, 27, 27, 1, 1, 1, 8, 14, 15, 57, 57, 1] 201
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 21, 24, 25, 26] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 27, 28, 29, 30, 31])
total number of confs: 328
number of broken/clashed sets: 37
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040738 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040738
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040738/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040738
Building REAL300000040739
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040739'
/scratch/stefan/7769621/working/building/REAL300000040739 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040739

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040739/0 /scratch/stefan/7769621/working/building/REAL300000040739 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 839)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/839
`/scratch/stefan/7769621/working/3D/839' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(COC2=CC=C(C=NNC(=O)NCC(F)(F)F)C=C2)OC=C1)

`REAL300000040739.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040739.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040739/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040739 none O=C([O-])C1=C(COC2=CC=C(C=NNC(=O)NCC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', '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, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [13, 10, 13, 9, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 34, 34, 34, 34, 77, 77, 77, 77, 1, 1, 9, 9, 9, 5, 5, 1, 1, 11, 34, 34, 77, 77, 1, 1, 9, 9] 147
rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 22, 23, 29, 30, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 38, 39])
total number of confs: 293
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040739 none O=C([O-])C1=C(COC2=CC=C(C=NNC(=O)NCC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', '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, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 3, 1, 1, 1, 5, 9, 9, 9, 9, 9, 40, 40, 82, 82, 82, 82, 147, 147, 147, 147, 9, 9, 1, 1, 1, 5, 5, 10, 10, 40, 82, 82, 147, 147, 9, 9, 1, 1] 147
rigid atoms, others: [1, 3, 4, 5, 38, 39, 24, 25, 26] set([0, 2, 6, 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])
total number of confs: 531
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040739 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040739
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040739/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040739
Building REAL300000040740
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040740'
/scratch/stefan/7769621/working/building/REAL300000040740 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040740

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040740/0 /scratch/stefan/7769621/working/building/REAL300000040740 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 840)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/840
`/scratch/stefan/7769621/working/3D/840' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNC(=O)NCC(F)(F)F)C(OCC(=O)[O-])=C1)

`REAL300000040740.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040740.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040740/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040740 none COC1=CC=C(C=NNC(=O)NCC(F)(F)F)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.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 9, 9, 9, 9, 50, 50, 50, 50, 1, 1, 9, 42, 75, 75, 1, 3, 3, 3, 1, 1, 4, 9, 9, 50, 50, 42, 42, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 17, 18, 23, 36, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 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
/scratch/stefan/7769621/working/building/REAL300000040740 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040740
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040740/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040740
Building REAL300000040741
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040741'
/scratch/stefan/7769621/working/building/REAL300000040741 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040741

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040741/0 /scratch/stefan/7769621/working/building/REAL300000040741 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 841)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/841
`/scratch/stefan/7769621/working/3D/841' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C(F)(F)OC1=CC=C(C=NNC(=O)NCC(F)(F)F)C=C1)

`REAL300000040741.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040741.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040741/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040741 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC(=O)NCC(F)(F)F)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [48, 29, 48, 7, 29, 29, 1, 1, 1, 1, 1, 1, 6, 6, 16, 17, 17, 17, 65, 65, 65, 65, 1, 1, 1, 1, 6, 16, 17, 65, 65, 1, 1] 201
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30])
total number of confs: 390
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040741 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040741
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040741/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040741
Building REAL300000040742
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040742'
/scratch/stefan/7769621/working/building/REAL300000040742 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040742

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040742/0 /scratch/stefan/7769621/working/building/REAL300000040742 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 842)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/842
`/scratch/stefan/7769621/working/3D/842' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(C(=O)[O-])=CC(Br)=C1C=NNC(=O)NCC(F)(F)F)

`REAL300000040742.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040742.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040742/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040742 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC(=O)NCC(F)(F)F 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.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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, 1, 11, 8, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 12, 12, 33, 33, 33, 33, 61, 61, 61, 61, 2, 2, 2, 1, 12, 33, 33, 61, 61] 61
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 24] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29])
total number of confs: 233
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040742 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040742
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040742/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040742
Building REAL300000040743
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040743'
/scratch/stefan/7769621/working/building/REAL300000040743 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040743

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040743/0 /scratch/stefan/7769621/working/building/REAL300000040743 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 843)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/843
`/scratch/stefan/7769621/working/3D/843' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC(=O)NCC(F)(F)F)C=C1Br)

`REAL300000040743.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040743.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040743/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040743 none O=C([O-])COC1=CC=C(C=NNC(=O)NCC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Br', '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, 11, 8, 5, 5, 15, 15, 15, 1, 1, 17, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [59, 33, 59, 8, 1, 1, 1, 1, 1, 1, 6, 6, 16, 17, 17, 17, 67, 67, 67, 67, 1, 1, 1, 33, 33, 1, 1, 6, 16, 17, 67, 67, 1] 201
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 20, 21, 22, 25, 26] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 27, 28, 29, 30, 31])
total number of confs: 420
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040743 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040743
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040743/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040743
Building REAL300000040744
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040744'
/scratch/stefan/7769621/working/building/REAL300000040744 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040744

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040744/0 /scratch/stefan/7769621/working/building/REAL300000040744 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 844)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/844
`/scratch/stefan/7769621/working/3D/844' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC(=O)NCC(F)(F)F)C=C1)

`REAL300000040744.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040744.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040744/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040744 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC(=O)NCC(F)(F)F)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.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 4, 4, 14, 14, 14, 14, 40, 40, 40, 40, 1, 1, 3, 3, 3, 1, 4, 14, 14, 40, 40, 1, 1] 40
rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 34, 35, 23, 24, 28] set([0, 32, 33, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 29, 30, 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/7769621/working/building/REAL300000040744 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040744
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040744/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040744
Building REAL300000040745
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040745'
/scratch/stefan/7769621/working/building/REAL300000040745 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040745

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040745/0 /scratch/stefan/7769621/working/building/REAL300000040745 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 845)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/845
`/scratch/stefan/7769621/working/3D/845' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC(=O)NCC(F)(F)F)C1=CC=C(C(=O)[O-])C=C1)

`REAL300000040745.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040745.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040745/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040745 none CCC(=NNC(=O)NCC(F)(F)F)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [18, 7, 1, 7, 7, 36, 36, 36, 36, 65, 65, 65, 65, 1, 1, 1, 1, 1, 2, 2, 1, 1, 18, 18, 18, 18, 18, 36, 36, 65, 65, 1, 1, 1, 1] 73
rigid atoms, others: [32, 33, 2, 34, 13, 14, 15, 16, 17, 20, 21, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 284
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040745 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040745
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040745/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040745
Building REAL300000040746
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040746'
/scratch/stefan/7769621/working/building/REAL300000040746 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040746

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040746/0 /scratch/stefan/7769621/working/building/REAL300000040746 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 846)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/846
`/scratch/stefan/7769621/working/3D/846' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NCC(F)(F)F)C1=CC=CC=C1C(=O)[O-])

`REAL300000040746.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040746.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040746/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040746 none CC(=NNC(=O)NCC(F)(F)F)C1=CC=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 5, 17, 17, 17, 17, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 17, 17, 34, 34, 1, 1, 1, 1] 34
rigid atoms, others: [1, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 133
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040746 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040746
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040746/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040746
Building REAL300000040747
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040747'
/scratch/stefan/7769621/working/building/REAL300000040747 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040747

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040747/0 /scratch/stefan/7769621/working/building/REAL300000040747 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 847)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/847
`/scratch/stefan/7769621/working/3D/847' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NCC(F)(F)F)C1=CC(C(=O)[O-])=CC=C1O)

`REAL300000040747.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040747.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040747/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040747 none CC(=NNC(=O)NCC(F)(F)F)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 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]
1  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: [11, 1, 11, 11, 39, 39, 39, 39, 61, 61, 61, 61, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 11, 11, 11, 39, 39, 61, 61, 1, 1, 1, 2] 122
rigid atoms, others: [1, 12, 13, 14, 15, 18, 19, 20, 21, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 218
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040747 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040747
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040747/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040747
Building REAL300000040748
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040748'
/scratch/stefan/7769621/working/building/REAL300000040748 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040748

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040748/0 /scratch/stefan/7769621/working/building/REAL300000040748 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 848)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/848
`/scratch/stefan/7769621/working/3D/848' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC(=O)NCC(F)(F)F)C1=CC(C(=O)[O-])=CC=C1F)

`REAL300000040748.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040748.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040748/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040748 none CCC(=NNC(=O)NCC(F)(F)F)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 12, 1, 12, 12, 62, 63, 63, 63, 144, 144, 144, 144, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 36, 36, 36, 36, 36, 62, 63, 144, 144, 1, 1, 1] 164
rigid atoms, others: [32, 33, 2, 34, 13, 14, 15, 16, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 637
number of broken/clashed sets: 50
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040748 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040748
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040748/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040748
Building REAL300000040749
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040749'
/scratch/stefan/7769621/working/building/REAL300000040749 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040749

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040749/0 /scratch/stefan/7769621/working/building/REAL300000040749 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 849)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/849
`/scratch/stefan/7769621/working/3D/849' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=NNC(C=NNC(=O)NCC(F)(F)F)=C2C=C1)

`REAL300000040749.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040749.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040749/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040749 none O=C([O-])C1=CC2=NNC(C=NNC(=O)NCC(F)(F)F)=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 7, 6, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 15, 15, 15, 23, 23, 23, 23, 1, 1, 1, 1, 1, 4, 15, 15, 23, 23, 1, 1] 23
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29])
total number of confs: 76
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040749 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040749/1 /scratch/stefan/7769621/working/building/REAL300000040749 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 850)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/850
`/scratch/stefan/7769621/working/3D/850' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(C=NNC(=O)NCC(F)(F)F)=NNC2=C1)

`REAL300000040749.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040749.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040749/1/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: REAL300000040749 none O=C([O-])C1=CC=C2C(C=NNC(=O)NCC(F)(F)F)=NNC2=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', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 8, 8, 1, 1, 7, 7, 7, 6, 6, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 42, 43, 43, 43, 66, 66, 66, 66, 1, 1, 1, 1, 1, 1, 12, 42, 43, 66, 66, 1, 1] 66
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29])
total number of confs: 235
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040749 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040749
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040749/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040749/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040749
Building REAL300000040750
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040750'
/scratch/stefan/7769621/working/building/REAL300000040750 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040750

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040750/0 /scratch/stefan/7769621/working/building/REAL300000040750 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 851)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/851
`/scratch/stefan/7769621/working/3D/851' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NCC(F)(F)F)C1=CC=CC(C(=O)[O-])=C1)

`REAL300000040750.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040750.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040750/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040750 none CC(=NNC(=O)NCC(F)(F)F)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 1, 11, 11, 27, 27, 27, 27, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 11, 11, 27, 27, 45, 45, 1, 1, 1, 1] 45
rigid atoms, others: [1, 12, 13, 14, 15, 16, 17, 20, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 175
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040750 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040750
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040750/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040750
Building REAL300000040751
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040751'
/scratch/stefan/7769621/working/building/REAL300000040751 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040751

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040751/0 /scratch/stefan/7769621/working/building/REAL300000040751 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 852)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/852
`/scratch/stefan/7769621/working/3D/852' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NCC(F)(F)F)C1=CC=C(C(=O)[O-])C(F)=C1)

`REAL300000040751.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040751.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040751/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040751 none CC(=NNC(=O)NCC(F)(F)F)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [11, 1, 11, 11, 57, 57, 57, 57, 126, 126, 126, 126, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 11, 11, 11, 57, 57, 126, 126, 1, 1, 1] 126
rigid atoms, others: [1, 12, 13, 14, 15, 16, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 444
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040751 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040751
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040751/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040751
Building REAL300000040752
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040752'
/scratch/stefan/7769621/working/building/REAL300000040752 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040752

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040752/0 /scratch/stefan/7769621/working/building/REAL300000040752 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 853)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/853
`/scratch/stefan/7769621/working/3D/853' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)NCC(F)(F)F)=C([N+](=O)[O-])C=C1OCC(=O)[O-])

`REAL300000040752.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040752.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040752/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040752 none COC1=CC(C=NNC(=O)NCC(F)(F)F)=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.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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]
0  hydrogens 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, 9, 9, 9, 9, 38, 38, 38, 38, 1, 1, 2, 2, 1, 1, 1, 10, 45, 67, 67, 3, 3, 3, 1, 6, 9, 9, 38, 38, 1, 45, 45] 201
rigid atoms, others: [1, 2, 3, 4, 5, 16, 17, 20, 21, 22, 36, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 361
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040752 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040752
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040752/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040752
Building REAL300000040753
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040753'
/scratch/stefan/7769621/working/building/REAL300000040753 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040753

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040753/0 /scratch/stefan/7769621/working/building/REAL300000040753 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 854)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/854
`/scratch/stefan/7769621/working/3D/854' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NCC(F)(F)F)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1)

`REAL300000040753.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040753.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040753/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040753 none CC(=NNC(=O)NCC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [70, 19, 70, 70, 113, 113, 113, 113, 201, 201, 201, 201, 7, 19, 19, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 19, 19, 70, 70, 70, 113, 113, 201, 201, 19, 19, 1, 1, 1, 1, 19, 19] 201
rigid atoms, others: [37, 38, 39, 40, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42])
total number of confs: 768
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040753 none CC(=NNC(=O)NCC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 6, 6, 23, 23, 23, 23, 69, 69, 69, 69, 1, 1, 1, 1, 1, 9, 19, 19, 9, 9, 19, 19, 19, 19, 1, 1, 6, 6, 6, 23, 23, 69, 69, 1, 1, 19, 19, 19, 19, 1, 1] 201
rigid atoms, others: [1, 35, 36, 41, 42, 12, 13, 14, 15, 16, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40])
total number of confs: 325
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040753 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040753
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040753/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040753
Building REAL300000040754
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040754'
/scratch/stefan/7769621/working/building/REAL300000040754 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040754

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040754/0 /scratch/stefan/7769621/working/building/REAL300000040754 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 855)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/855
`/scratch/stefan/7769621/working/3D/855' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)NCC(F)(F)F)=CC=C1OCCC(=O)[O-])

`REAL300000040754.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040754.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040754/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040754 none COC1=CC(C=NNC(=O)NCC(F)(F)F)=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.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 7, 7, 7, 37, 37, 37, 37, 1, 1, 1, 1, 9, 35, 39, 60, 57, 3, 3, 3, 1, 7, 7, 7, 37, 37, 1, 1, 35, 35, 39, 39] 201
rigid atoms, others: [19, 1, 2, 3, 4, 5, 34, 16, 17, 18, 35, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 36, 37, 38, 39])
total number of confs: 336
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040754 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040754
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040754/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040754
Building REAL300000040755
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040755'
/scratch/stefan/7769621/working/building/REAL300000040755 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040755

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040755/0 /scratch/stefan/7769621/working/building/REAL300000040755 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 856)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/856
`/scratch/stefan/7769621/working/3D/856' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC(=O)NCC(F)(F)F)C(Cl)=C1)

`REAL300000040755.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040755.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040755/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040755 none O=C([O-])C1=CC=C(C=NNC(=O)NCC(F)(F)F)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 16, 1, 7, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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: [2, 1, 2, 1, 1, 1, 1, 1, 10, 10, 24, 24, 24, 24, 33, 33, 33, 33, 1, 1, 1, 1, 1, 10, 24, 24, 33, 33, 1] 33
rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27])
total number of confs: 108
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040755 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040755
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040755/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040755
Building REAL300000040756
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040756'
/scratch/stefan/7769621/working/building/REAL300000040756 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040756

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040756/0 /scratch/stefan/7769621/working/building/REAL300000040756 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 857)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/857
`/scratch/stefan/7769621/working/3D/857' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NCC(F)(F)F)C1=CC(C(=O)[O-])=C(C)N=C1C)

`REAL300000040756.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040756.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040756/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040756 none CC(=NNC(=O)NCC(F)(F)F)C1=CC(C(=O)[O-])=C(C)N=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 31, 31, 31, 31, 93, 93, 93, 93, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 9, 9, 9, 31, 31, 93, 93, 1, 2, 2, 2, 2, 2, 2] 93
rigid atoms, others: [1, 12, 13, 14, 15, 18, 19, 20, 21, 22, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36])
total number of confs: 361
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040756 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040756
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040756/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040756
Building REAL300000040757
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040757'
/scratch/stefan/7769621/working/building/REAL300000040757 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040757

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040757/0 /scratch/stefan/7769621/working/building/REAL300000040757 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 858)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/858
`/scratch/stefan/7769621/working/3D/858' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C=NNC(=O)NCC(F)(F)F)=CC=C1O)

`REAL300000040757.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040757.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040757/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040757 none O=C([O-])C1=CC(C=NNC(=O)NCC(F)(F)F)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 12, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 7, 7, 21, 22, 22, 22, 46, 46, 46, 46, 1, 1, 1, 1, 1, 7, 21, 22, 46, 46, 1, 1, 2] 92
rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 21, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 29])
total number of confs: 168
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040757 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040757
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040757/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040757
Building REAL300000040758
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040758'
/scratch/stefan/7769621/working/building/REAL300000040758 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040758

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040758/0 /scratch/stefan/7769621/working/building/REAL300000040758 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 859)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/859
`/scratch/stefan/7769621/working/3D/859' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NCC(F)(F)F)C1=CC(C(=O)[O-])=CC=C1C)

`REAL300000040758.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040758.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040758/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040758 none CC(=NNC(=O)NCC(F)(F)F)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 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
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [9, 1, 9, 9, 27, 27, 27, 27, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 27, 27, 47, 47, 1, 1, 1, 2, 2, 2] 47
rigid atoms, others: [1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 33, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 185
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040758 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040758
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040758/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040758
Building REAL300000040759
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040759'
/scratch/stefan/7769621/working/building/REAL300000040759 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040759

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040759/0 /scratch/stefan/7769621/working/building/REAL300000040759 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 860)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/860
`/scratch/stefan/7769621/working/3D/860' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=C(C=NNC(=O)NCC(F)(F)F)C=C1)C(=O)[O-])

`REAL300000040759.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040759.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040759/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040759 none CC(OC1=CC=C(C=NNC(=O)NCC(F)(F)F)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.am', 'C.2', 'O.2', 'N.am', 'C.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', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 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]
0  hydrogens 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, 1, 1, 1, 1, 1, 1, 8, 8, 22, 23, 23, 23, 97, 97, 97, 97, 1, 1, 16, 25, 25, 16, 16, 16, 16, 1, 1, 8, 22, 23, 97, 97, 1, 1] 201
rigid atoms, others: [35, 2, 3, 4, 5, 6, 7, 34, 18, 19, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33])
total number of confs: 419
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040759 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040759
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040759/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040759
Building REAL300000040760
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040760'
/scratch/stefan/7769621/working/building/REAL300000040760 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040760

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040760/0 /scratch/stefan/7769621/working/building/REAL300000040760 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 861)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/861
`/scratch/stefan/7769621/working/3D/861' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1CCC(=NNC(=O)NCC(F)(F)F)C2=CC=CC=C21)

`REAL300000040760.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040760.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040760/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040760 none O=C([O-])C1CCC(=NNC(=O)NCC(F)(F)F)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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: [11, 1, 11, 5, 5, 5, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 15, 15, 1, 1, 1, 1] 15
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31])
total number of confs: 53
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040760 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040760
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040760/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040760
Building REAL300000040761
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040761'
/scratch/stefan/7769621/working/building/REAL300000040761 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040761

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040761/0 /scratch/stefan/7769621/working/building/REAL300000040761 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 862)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/862
`/scratch/stefan/7769621/working/3D/862' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CN1C=C(C=NNC(=O)NCC(F)(F)F)C2=CC=CC=C21)

`REAL300000040761.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040761.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040761/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040761 none O=C([O-])CN1C=C(C=NNC(=O)NCC(F)(F)F)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 8, 15, 1, 1, 1, 1, 1, 10, 10, 41, 41, 41, 41, 123, 123, 123, 123, 1, 1, 1, 1, 1, 1, 8, 8, 1, 10, 40, 41, 123, 123, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 26, 35] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 27, 28, 29, 30, 31])
total number of confs: 478
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040761 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040761
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040761/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040761
Building REAL300000040762
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040762'
/scratch/stefan/7769621/working/building/REAL300000040762 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040762

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040762/0 /scratch/stefan/7769621/working/building/REAL300000040762 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 863)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/863
`/scratch/stefan/7769621/working/3D/863' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NCC(F)(F)F)C1=CC=CC(OCCCC(=O)[O-])=C1)

`REAL300000040762.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040762.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040762/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040762 none CC(=NNC(=O)NCC(F)(F)F)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 10, 10, 15, 15, 15, 15, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 7, 15, 23, 31, 45, 45, 1, 10, 10, 10, 15, 15, 49, 49, 1, 1, 1, 15, 15, 23, 23, 31, 31, 1] 201
rigid atoms, others: [32, 1, 34, 33, 41, 12, 13, 14, 15, 16, 17, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40])
total number of confs: 355
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040762 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040762
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040762/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040762
Building REAL300000040763
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040763'
/scratch/stefan/7769621/working/building/REAL300000040763 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040763

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040763/0 /scratch/stefan/7769621/working/building/REAL300000040763 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 864)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/864
`/scratch/stefan/7769621/working/3D/864' -> `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)=NNC(=O)NCC(F)(F)F)

`REAL300000040763.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040763.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040763/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040763 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)=NNC(=O)NCC(F)(F)F 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', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 1, 1, 1, 1, 1, 1, 1, 9, 21, 21, 27, 27, 1, 1, 6, 6, 17, 17, 17, 17, 76, 76, 76, 76, 6, 6, 6, 3, 3, 1, 1, 1, 1, 21, 21, 21, 21, 1, 1, 17, 17, 76, 76] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 39, 34, 14, 15, 40, 31] set([0, 1, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 41, 42, 43, 44])
total number of confs: 359
number of broken/clashed sets: 163
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040763 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040763
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040763/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040763
Building REAL300000040764
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040764'
/scratch/stefan/7769621/working/building/REAL300000040764 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040764

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040764/0 /scratch/stefan/7769621/working/building/REAL300000040764 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 865)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/865
`/scratch/stefan/7769621/working/3D/865' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CC=C(OCC(=O)[O-])C=C1)=NNC(=O)NCC(F)(F)F)

`REAL300000040764.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040764.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040764/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040764 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)=NNC(=O)NCC(F)(F)F 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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 4, 2, 1, 1, 1, 1, 1, 1, 6, 16, 26, 26, 1, 1, 5, 5, 13, 13, 13, 13, 49, 49, 49, 49, 5, 5, 5, 4, 4, 2, 2, 1, 1, 16, 16, 1, 1, 13, 13, 49, 49] 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])
total number of confs: 270
number of broken/clashed sets: 195
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040764 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040764
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040764/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040764
Building REAL300000040765
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040765'
/scratch/stefan/7769621/working/building/REAL300000040765 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040765

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040765/0 /scratch/stefan/7769621/working/building/REAL300000040765 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 866)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/866
`/scratch/stefan/7769621/working/3D/866' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NCC(F)(F)F)C1=CC=CC(OC(C)C(=O)[O-])=C1)

`REAL300000040765.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040765.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040765/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040765 none CC(=NNC(=O)NCC(F)(F)F)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [8, 1, 8, 8, 14, 14, 14, 14, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 11, 26, 26, 37, 37, 1, 8, 8, 8, 14, 14, 53, 53, 1, 1, 1, 26, 26, 26, 26, 1] 201
rigid atoms, others: [32, 1, 38, 33, 12, 13, 14, 15, 16, 17, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37])
total number of confs: 302
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040765 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040765
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040765/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040765
Building REAL300000040766
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040766'
/scratch/stefan/7769621/working/building/REAL300000040766 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040766

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040766/0 /scratch/stefan/7769621/working/building/REAL300000040766 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 867)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/867
`/scratch/stefan/7769621/working/3D/867' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)=NNC(=O)NCC(F)(F)F)

`REAL300000040766.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040766.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040766/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040766 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)=NNC(=O)NCC(F)(F)F 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', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 1, 1, 1, 1, 1, 1, 1, 6, 10, 12, 21, 19, 1, 1, 11, 11, 19, 19, 19, 19, 56, 56, 56, 56, 11, 11, 11, 3, 3, 1, 1, 1, 1, 10, 10, 12, 12, 1, 1, 19, 19, 56, 56] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 39, 34, 14, 15, 40, 31] set([0, 1, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 41, 42, 43, 44])
total number of confs: 268
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040766 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040766
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040766/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040766
Building REAL300000040767
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040767'
/scratch/stefan/7769621/working/building/REAL300000040767 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040767

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040767/0 /scratch/stefan/7769621/working/building/REAL300000040767 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 868)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/868
`/scratch/stefan/7769621/working/3D/868' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC(=O)NCC(F)(F)F)C1=CC=C(OCCCCC(=O)[O-])C=C1)

`REAL300000040767.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040767.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040767/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040767 none CCC(=NNC(=O)NCC(F)(F)F)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 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, 6, 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, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 1, 5, 5, 5, 5, 5, 5, 27, 27, 27, 27, 1, 1, 1, 1, 1, 6, 9, 23, 28, 43, 49, 52, 1, 1, 7, 7, 7, 7, 7, 5, 5, 27, 27, 1, 1, 9, 9, 23, 23, 28, 28, 43, 43, 1, 1] 201
rigid atoms, others: [2, 36, 37, 13, 14, 15, 16, 17, 46, 25, 26, 47] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 323
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040767 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040767
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040767/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040767
Building REAL300000040768
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040768'
/scratch/stefan/7769621/working/building/REAL300000040768 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040768

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040768/0 /scratch/stefan/7769621/working/building/REAL300000040768 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 869)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/869
`/scratch/stefan/7769621/working/3D/869' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NCC(F)(F)F)C1=CSC(C(=O)[O-])=C1)

`REAL300000040768.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040768.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040768/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040768 none CC(=NNC(=O)NCC(F)(F)F)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [12, 1, 12, 12, 30, 30, 30, 30, 52, 52, 52, 52, 1, 1, 1, 1, 1, 2, 2, 1, 12, 12, 12, 30, 30, 52, 52, 1, 1] 52
rigid atoms, others: [1, 12, 13, 14, 15, 16, 19, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 197
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040768 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040768
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040768/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040768
Building REAL300000040769
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040769'
/scratch/stefan/7769621/working/building/REAL300000040769 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040769

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040769/0 /scratch/stefan/7769621/working/building/REAL300000040769 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 870)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/870
`/scratch/stefan/7769621/working/3D/870' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1(C2=CC=CC=C2)CC(=NNC(=O)NCC(F)(F)F)C1)

`REAL300000040769.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040769.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040769/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040769 none O=C([O-])C1(C2=CC=CC=C2)CC(=NNC(=O)NCC(F)(F)F)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.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', '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, 5, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [9, 7, 9, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 25, 25, 25, 25, 57, 57, 57, 57, 7, 1, 1, 1, 1, 1, 7, 7, 25, 25, 57, 57, 7, 7] 57
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 215
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040769 none O=C([O-])C1(C2=CC=CC=C2)CC(=NNC(=O)NCC(F)(F)F)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.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', '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, 5, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 7, 7, 1, 7, 7, 1, 1, 1, 1, 8, 9, 9, 9, 34, 34, 34, 34, 1, 7, 7, 1, 7, 7, 1, 1, 8, 9, 34, 34, 1, 1] 57
rigid atoms, others: [1, 34, 3, 4, 10, 11, 12, 13, 35, 22, 28, 29] set([0, 2, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33])
total number of confs: 138
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040769 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040769
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040769/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040769
Building REAL300000040770
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040770'
/scratch/stefan/7769621/working/building/REAL300000040770 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040770

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040770/0 /scratch/stefan/7769621/working/building/REAL300000040770 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 871)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/871
`/scratch/stefan/7769621/working/3D/871' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NCC(F)(F)F)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C)

`REAL300000040770.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040770.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040770/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040770 none CC(=NNC(=O)NCC(F)(F)F)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 7, 29, 29, 29, 29, 77, 77, 77, 77, 1, 1, 1, 1, 1, 1, 7, 15, 15, 1, 1, 1, 7, 7, 7, 29, 29, 77, 77, 1, 1, 7, 7, 2, 2, 2, 2, 2, 2] 110
rigid atoms, others: [32, 1, 12, 13, 14, 15, 16, 17, 21, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 330
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040770 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040770
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040770/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040770
Building REAL300000040771
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040771'
/scratch/stefan/7769621/working/building/REAL300000040771 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040771

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040771/0 /scratch/stefan/7769621/working/building/REAL300000040771 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 872)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/872
`/scratch/stefan/7769621/working/3D/872' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCCCCCC(=O)[O-])=NNC(=O)NCC(F)(F)F)

`REAL300000040771.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040771.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040771/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.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: REAL300000040771 none CC(CCCCCCC(=O)[O-])=NNC(=O)NCC(F)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', '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']
dock atom type numbers: [5, 1, 5, 5, 5, 5, 5, 5, 1, 11, 11, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 6, 4, 7, 7, 7, 7, 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: [7, 1, 1, 1, 3, 5, 5, 7, 10, 10, 10, 7, 7, 9, 9, 9, 9, 20, 20, 20, 20, 7, 7, 7, 1, 1, 3, 3, 5, 5, 5, 5, 7, 7, 10, 10, 9, 9, 20, 20] 31
rigid atoms, others: [24, 1, 2, 3, 25] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 119
number of broken/clashed sets: 31
./output.0.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040771 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040771
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040771/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040771
Building REAL300000040772
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040772'
/scratch/stefan/7769621/working/building/REAL300000040772 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040772

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040772/0 /scratch/stefan/7769621/working/building/REAL300000040772 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 873)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/873
`/scratch/stefan/7769621/working/3D/873' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NCC(F)(F)F)C1=CC(C(=O)[O-])=CS1)

`REAL300000040772.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040772.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040772/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040772 none CC(=NNC(=O)NCC(F)(F)F)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 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]
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: [13, 1, 12, 12, 40, 40, 40, 40, 66, 66, 66, 66, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 39, 40, 66, 66, 1, 1] 66
rigid atoms, others: [1, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 240
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040772 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040772
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040772/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040772
Building REAL300000040773
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040773'
/scratch/stefan/7769621/working/building/REAL300000040773 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040773

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040773/0 /scratch/stefan/7769621/working/building/REAL300000040773 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 874)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/874
`/scratch/stefan/7769621/working/3D/874' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(=NNC(=O)NCC(F)(F)F)CCC(C(=O)[O-])C1(C)C)

`REAL300000040773.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040773.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040773/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040773 none CC1C(=NNC(=O)NCC(F)(F)F)CCC(C(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.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, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 8, 8, 8, 8, 15, 15, 15, 15, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 2, 1, 8, 8, 15, 15, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 15
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 13, 14, 15, 16, 34, 19, 20, 21, 25, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 22, 23, 24, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40])
total number of confs: 72
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040773 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040773
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040773/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040773
Building REAL300000040774
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040774'
/scratch/stefan/7769621/working/building/REAL300000040774 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040774

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040774/0 /scratch/stefan/7769621/working/building/REAL300000040774 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 875)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/875
`/scratch/stefan/7769621/working/3D/875' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(C)=NNC(=O)NCC(F)(F)F)=CC=C1OCCCC(=O)[O-])

`REAL300000040774.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040774.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040774/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040774 none COC1=CC(C(C)=NNC(=O)NCC(F)(F)F)=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.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 4, 4, 4, 8, 8, 8, 8, 26, 26, 26, 26, 1, 1, 1, 1, 7, 28, 40, 57, 64, 64, 3, 3, 3, 1, 5, 5, 5, 8, 8, 26, 26, 1, 1, 28, 28, 40, 40, 57, 57] 201
rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 17, 18, 19, 20, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45])
total number of confs: 365
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040774 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040774
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040774/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040774
Building REAL300000040775
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040775'
/scratch/stefan/7769621/working/building/REAL300000040775 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040775

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040775/0 /scratch/stefan/7769621/working/building/REAL300000040775 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 876)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/876
`/scratch/stefan/7769621/working/3D/876' -> `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(=NNC(=O)NCC(F)(F)F)C1)

`REAL300000040775.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040775.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040775/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040775 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(=NNC(=O)NCC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', '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, 8, 1, 11, 8, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [17, 11, 17, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 37, 37, 37, 37, 95, 95, 95, 95, 11, 1, 1, 1, 1, 11, 11, 37, 37, 95, 95, 11, 11] 95
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 366
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040775 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(=NNC(=O)NCC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', '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, 8, 1, 11, 8, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 11, 11, 3, 11, 11, 11, 1, 1, 1, 1, 6, 7, 7, 7, 33, 33, 33, 33, 1, 11, 11, 9, 11, 1, 1, 6, 7, 33, 33, 1, 1] 95
rigid atoms, others: [1, 34, 3, 4, 11, 12, 13, 14, 35, 23, 28, 29] set([0, 2, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 30, 31, 32, 33])
total number of confs: 153
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040775 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040775
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040775/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040775
Building REAL300000040776
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040776'
/scratch/stefan/7769621/working/building/REAL300000040776 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040776

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040776/0 /scratch/stefan/7769621/working/building/REAL300000040776 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 877)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/877
`/scratch/stefan/7769621/working/3D/877' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC(=O)NCC(F)(F)F)

`REAL300000040776.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040776.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040776/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040776 none O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC(=O)NCC(F)(F)F 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', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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, 5, 5, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 14, 14] 14
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([32, 33, 34, 35, 15, 16, 17, 18, 19, 20, 21, 22])
total number of confs: 47
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040776 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040776
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040776/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040776
Building REAL300000040777
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040777'
/scratch/stefan/7769621/working/building/REAL300000040777 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040777

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040777/0 /scratch/stefan/7769621/working/building/REAL300000040777 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 878)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/878
`/scratch/stefan/7769621/working/3D/878' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NCC(F)(F)F)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1)

`REAL300000040777.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040777.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040777/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040777 none CC(=NNC(=O)NCC(F)(F)F)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 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]
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, 36, 36, 36, 36, 66, 66, 66, 66, 1, 1, 1, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 36, 36, 66, 66, 2, 2, 1, 1, 2, 2, 2, 1] 70
rigid atoms, others: [1, 35, 36, 40, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39])
total number of confs: 259
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040777 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040777
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040777/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040777
Building REAL300000040778
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040778'
/scratch/stefan/7769621/working/building/REAL300000040778 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040778

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040778/0 /scratch/stefan/7769621/working/building/REAL300000040778 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 879)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/879
`/scratch/stefan/7769621/working/3D/879' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC(=O)NCC(F)(F)F)

`REAL300000040778.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040778.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040778/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040778 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC(=O)NCC(F)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 13, 13, 38, 38, 38, 38, 60, 60, 60, 60, 2, 2, 2, 1, 2, 2, 2, 1, 13, 38, 38, 60, 60] 60
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 25, 29] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34])
total number of confs: 228
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040778 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040778
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040778/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040778
Building REAL300000040779
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040779'
/scratch/stefan/7769621/working/building/REAL300000040779 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040779

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040779/0 /scratch/stefan/7769621/working/building/REAL300000040779 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 880)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/880
`/scratch/stefan/7769621/working/3D/880' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Cl)C(C=NNC(=O)NCC(F)(F)F)=CC=C1)

`REAL300000040779.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040779.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040779/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040779 none O=C([O-])C1=C(Cl)C(C=NNC(=O)NCC(F)(F)F)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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: [3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 16, 16, 16, 16, 36, 36, 36, 36, 1, 1, 1, 6, 16, 16, 36, 36, 1, 1, 1] 36
rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25])
total number of confs: 138
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040779 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040779
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040779/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040779
Building REAL300000040780
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040780'
/scratch/stefan/7769621/working/building/REAL300000040780 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040780

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040780/0 /scratch/stefan/7769621/working/building/REAL300000040780 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 881)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/881
`/scratch/stefan/7769621/working/3D/881' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC(=O)NCC(F)(F)F)

`REAL300000040780.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040780.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040780/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040780 none O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC(=O)NCC(F)(F)F 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', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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, 5, 5, 5, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 5, 6, 6, 6, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 6, 13, 13] 13
rigid atoms, others: [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] set([35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23])
total number of confs: 45
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040780 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040780
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040780/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040780
Building REAL300000040781
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040781'
/scratch/stefan/7769621/working/building/REAL300000040781 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040781

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040781/0 /scratch/stefan/7769621/working/building/REAL300000040781 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 882)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/882
`/scratch/stefan/7769621/working/3D/882' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C(OC1=CC(C=NNC(=O)NCC(F)(F)F)=CC=C1)C1=CC=CC=C1)

`REAL300000040781.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040781.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040781/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040781 none O=C([O-])C(OC1=CC(C=NNC(=O)NCC(F)(F)F)=CC=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.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 44, 44, 44, 96, 96, 108, 108, 108, 108, 201, 201, 201, 201, 44, 44, 44, 1, 1, 1, 1, 1, 1, 3, 44, 96, 108, 108, 201, 201, 44, 44, 44, 1, 1, 1, 1, 1] 201
rigid atoms, others: [3, 38, 39, 40, 41, 42, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 753
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040781 none O=C([O-])C(OC1=CC(C=NNC(=O)NCC(F)(F)F)=CC=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.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 41, 11, 1, 1, 1, 1, 1, 4, 4, 7, 8, 8, 8, 36, 36, 36, 36, 1, 1, 1, 32, 44, 44, 32, 44, 44, 32, 1, 4, 7, 8, 36, 36, 1, 1, 1, 44, 44, 32, 44, 44] 201
rigid atoms, others: [35, 4, 5, 6, 7, 8, 19, 20, 21, 36, 29, 37] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42])
total number of confs: 325
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040781 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040781
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040781/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040781
Building REAL300000040782
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040782'
/scratch/stefan/7769621/working/building/REAL300000040782 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040782

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040782/0 /scratch/stefan/7769621/working/building/REAL300000040782 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 883)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/883
`/scratch/stefan/7769621/working/3D/883' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC(=O)NCC(F)(F)F)C=C1F)

`REAL300000040782.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040782.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040782/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040782 none O=C([O-])C1=CC=C(C=NNC(=O)NCC(F)(F)F)C=C1F NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 15, 7, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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: [3, 1, 3, 1, 1, 1, 1, 1, 11, 11, 39, 39, 39, 39, 88, 88, 88, 88, 1, 1, 1, 1, 1, 11, 39, 39, 88, 88, 1] 88
rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27])
total number of confs: 293
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040782 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040782
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040782/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040782
Building REAL300000040783
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040783'
/scratch/stefan/7769621/working/building/REAL300000040783 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040783

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040783/0 /scratch/stefan/7769621/working/building/REAL300000040783 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 884)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/884
`/scratch/stefan/7769621/working/3D/884' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C=CC1=CC=C(C=NNC(=O)NCC(F)(F)F)O1)

`REAL300000040783.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040783.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040783/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040783 none O=C([O-])C=CC1=CC=C(C=NNC(=O)NCC(F)(F)F)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 3, 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: [33, 13, 34, 13, 1, 1, 1, 1, 1, 1, 6, 6, 22, 23, 23, 23, 86, 86, 86, 86, 1, 13, 13, 1, 1, 6, 22, 23, 86, 86] 134
rigid atoms, others: [4, 5, 6, 7, 8, 9, 20, 23, 24] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 25, 26, 27, 28, 29])
total number of confs: 390
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040783 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040783
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040783/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040783
Building REAL300000040784
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040784'
/scratch/stefan/7769621/working/building/REAL300000040784 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040784

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040784/0 /scratch/stefan/7769621/working/building/REAL300000040784 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 885)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/885
`/scratch/stefan/7769621/working/3D/885' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NCC(F)(F)F)C1=CC(C(=O)[O-])=CC=C1OC(C)C)

`REAL300000040784.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040784.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040784/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040784 none CC(=NNC(=O)NCC(F)(F)F)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 44, 44, 44, 44, 159, 159, 159, 159, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 21, 21, 11, 11, 11, 44, 44, 159, 159, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21] 201
rigid atoms, others: [32, 1, 34, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 627
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040784 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040784
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040784/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040784
Building REAL300000040785
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040785'
/scratch/stefan/7769621/working/building/REAL300000040785 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040785

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040785/0 /scratch/stefan/7769621/working/building/REAL300000040785 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 886)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/886
`/scratch/stefan/7769621/working/3D/886' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C2C(=CC=C1)CCC2=NNC(=O)NCC(F)(F)F)

`REAL300000040785.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040785.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040785/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040785 none O=C([O-])C1=C2C(=CC=C1)CCC2=NNC(=O)NCC(F)(F)F 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', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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, 5, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 10, 10, 10, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 9, 10, 18, 18] 18
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28] set([0, 32, 2, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31])
total number of confs: 66
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040785 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040785
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040785/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040785
Building REAL300000040786
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040786'
/scratch/stefan/7769621/working/building/REAL300000040786 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040786

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040786/0 /scratch/stefan/7769621/working/building/REAL300000040786 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 887)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/887
`/scratch/stefan/7769621/working/3D/887' -> `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=NNC(=O)NCC(F)(F)F)C=C2)C=C1)

`REAL300000040786.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040786.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040786/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040786 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC(=O)NCC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 12, 13, 13, 13, 41, 41, 41, 41, 1, 1, 3, 3, 3, 3, 1, 1, 6, 12, 13, 41, 41, 1, 1, 3, 3] 45
rigid atoms, others: [36, 6, 7, 8, 9, 10, 11, 35, 22, 23, 28, 29] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 156
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040786 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC(=O)NCC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 3, 3, 1, 3, 11, 11, 18, 18, 18, 18, 45, 45, 45, 45, 3, 3, 1, 1, 1, 1, 3, 3, 11, 18, 18, 45, 45, 3, 3, 1, 1] 45
rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 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: 174
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040786 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040786
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040786/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040786
Building REAL300000040787
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040787'
/scratch/stefan/7769621/working/building/REAL300000040787 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040787

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040787/0 /scratch/stefan/7769621/working/building/REAL300000040787 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 888)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/888
`/scratch/stefan/7769621/working/3D/888' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NCC(F)(F)F)C1=CN=CC(C(=O)[O-])=C1)

`REAL300000040787.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040787.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040787/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040787 none CC(=NNC(=O)NCC(F)(F)F)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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: [11, 1, 11, 11, 29, 29, 29, 29, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 11, 11, 29, 29, 49, 49, 1, 1, 1] 49
rigid atoms, others: [1, 12, 13, 14, 15, 16, 17, 20, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 185
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040787 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040787
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040787/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040787
Building REAL300000040788
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040788'
/scratch/stefan/7769621/working/building/REAL300000040788 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040788

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040788/0 /scratch/stefan/7769621/working/building/REAL300000040788 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 889)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/889
`/scratch/stefan/7769621/working/3D/889' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2NC=C(C=NNC(=O)NCC(F)(F)F)C2=C1)

`REAL300000040788.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040788.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040788/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040788 none O=C([O-])C1=CC=C2NC=C(C=NNC(=O)NCC(F)(F)F)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 14, 14, 14, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 4, 14, 14, 24, 24, 1] 24
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 21, 22, 23, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 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/7769621/working/building/REAL300000040788 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040788
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040788/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040788
Building REAL300000040789
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040789'
/scratch/stefan/7769621/working/building/REAL300000040789 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040789

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040789/0 /scratch/stefan/7769621/working/building/REAL300000040789 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 890)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/890
`/scratch/stefan/7769621/working/3D/890' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)NCC(F)(F)F)=CC(Cl)=C1OC(C)C(=O)[O-])

`REAL300000040789.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040789.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040789/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040789 none COC1=CC(C=NNC(=O)NCC(F)(F)F)=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.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 22, 23, 23, 23, 91, 91, 91, 91, 1, 1, 1, 1, 1, 5, 13, 13, 19, 19, 4, 4, 4, 1, 6, 22, 23, 91, 91, 1, 13, 13, 13, 13] 201
rigid atoms, others: [1, 2, 3, 4, 5, 35, 16, 17, 18, 19, 20, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 36, 37, 38, 39])
total number of confs: 387
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040789 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040789
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040789/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040789
Building REAL300000040790
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040790'
/scratch/stefan/7769621/working/building/REAL300000040790 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040790

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040790/0 /scratch/stefan/7769621/working/building/REAL300000040790 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 891)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/891
`/scratch/stefan/7769621/working/3D/891' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC(=O)NCC(F)(F)F)C=C1O)

`REAL300000040790.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040790.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040790/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040790 none O=C([O-])C1=CC=C(C=NNC(=O)NCC(F)(F)F)C=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 12, 7, 7, 7, 6, 6, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
152  conformations in input
total number of sets (complete confs): 152
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 10, 10, 38, 38, 38, 38, 76, 76, 76, 76, 1, 1, 1, 1, 1, 10, 38, 38, 76, 76, 1, 2] 152
rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 29])
total number of confs: 245
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040790 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040790
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040790/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040790
Building REAL300000040791
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040791'
/scratch/stefan/7769621/working/building/REAL300000040791 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040791

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040791/0 /scratch/stefan/7769621/working/building/REAL300000040791 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 892)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/892
`/scratch/stefan/7769621/working/3D/892' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C=NNC(=O)NCC(F)(F)F)C=C1C(=O)[O-])

`REAL300000040791.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040791.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040791/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040791 none CC1=CC=C(C=NNC(=O)NCC(F)(F)F)C=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.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, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7, 7, 7, 4, 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
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 61, 61, 61, 61, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 6, 22, 23, 61, 61, 1] 61
rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 18, 24, 25, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30])
total number of confs: 232
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040791 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040791
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040791/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040791
Building REAL300000040792
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040792'
/scratch/stefan/7769621/working/building/REAL300000040792 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040792

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040792/0 /scratch/stefan/7769621/working/building/REAL300000040792 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 893)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/893
`/scratch/stefan/7769621/working/3D/893' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Cl)SC(C=NNC(=O)NCC(F)(F)F)=C1)

`REAL300000040792.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040792.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040792/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040792 none O=C([O-])C1=C(Cl)SC(C=NNC(=O)NCC(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 10, 41, 42, 42, 42, 102, 102, 102, 102, 1, 10, 41, 42, 102, 102, 1] 102
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 25] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24])
total number of confs: 359
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040792 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040792
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040792/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040792
Building REAL300000040793
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040793'
/scratch/stefan/7769621/working/building/REAL300000040793 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040793

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040793/0 /scratch/stefan/7769621/working/building/REAL300000040793 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 894)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/894
`/scratch/stefan/7769621/working/3D/894' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NCC(F)(F)F)C1=CC=C(C(=O)[O-])C=C1C)

`REAL300000040793.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040793.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040793/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040793 none CC(=NNC(=O)NCC(F)(F)F)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 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
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [9, 1, 9, 9, 32, 32, 32, 32, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 32, 32, 50, 50, 1, 1, 1, 2, 2, 2] 50
rigid atoms, others: [1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 33, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 180
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040793 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040793
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040793/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040793
Building REAL300000040794
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040794'
/scratch/stefan/7769621/working/building/REAL300000040794 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040794

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040794/0 /scratch/stefan/7769621/working/building/REAL300000040794 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 895)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/895
`/scratch/stefan/7769621/working/3D/895' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C(Cl)C=C1C=NNC(=O)NCC(F)(F)F)

`REAL300000040794.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040794.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040794/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040794 none O=C([O-])C1=CN=C(Cl)C=C1C=NNC(=O)NCC(F)(F)F NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 16, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 13, 13, 13, 13, 25, 25, 25, 25, 1, 1, 6, 13, 13, 25, 25] 25
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27])
total number of confs: 97
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040794 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040794
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040794/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040794
Building REAL300000040795
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040795'
/scratch/stefan/7769621/working/building/REAL300000040795 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040795

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040795/0 /scratch/stefan/7769621/working/building/REAL300000040795 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 896)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/896
`/scratch/stefan/7769621/working/3D/896' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C2=CC=C(C=NNC(=O)NCC(F)(F)F)O2)=CC=C1O)

`REAL300000040795.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040795.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040795/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040795 none O=C([O-])C1=CC(C2=CC=C(C=NNC(=O)NCC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 8, 1, 11, 8, 5, 5, 15, 15, 15, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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: [25, 13, 25, 13, 13, 1, 1, 1, 1, 1, 1, 8, 8, 26, 27, 27, 27, 82, 82, 82, 82, 1, 13, 13, 12, 12, 13, 1, 1, 8, 26, 27, 82, 82, 13, 13, 26] 402
rigid atoms, others: [5, 6, 7, 8, 9, 10, 21, 27, 28] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 378
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040795 none O=C([O-])C1=CC(C2=CC=C(C=NNC(=O)NCC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 8, 1, 11, 8, 5, 5, 15, 15, 15, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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, 47, 47, 108, 108, 108, 108, 201, 201, 201, 201, 13, 1, 1, 1, 1, 1, 13, 13, 47, 108, 108, 201, 201, 1, 1, 2] 402
rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 36])
total number of confs: 740
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040795 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040795
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040795/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040795
Building REAL300000040796
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040796'
/scratch/stefan/7769621/working/building/REAL300000040796 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040796

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040796/0 /scratch/stefan/7769621/working/building/REAL300000040796 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 897)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/897
`/scratch/stefan/7769621/working/3D/897' -> `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=NNC(=O)NCC(F)(F)F)

`REAL300000040796.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040796.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040796/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040796 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC(=O)NCC(F)(F)F 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.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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, 1, 11, 8, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 12, 12, 29, 29, 29, 29, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 1, 1, 1, 12, 29, 29, 50, 50] 50
rigid atoms, others: [1, 3, 4, 5, 6, 7, 10, 11, 12, 29, 30, 31] set([0, 2, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36])
total number of confs: 188
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040796 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040796
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040796/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040796
Building REAL300000040797
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040797'
/scratch/stefan/7769621/working/building/REAL300000040797 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040797

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040797/0 /scratch/stefan/7769621/working/building/REAL300000040797 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 898)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/898
`/scratch/stefan/7769621/working/3D/898' -> `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=NNC(=O)NCC(F)(F)F)S2)C=C1)

`REAL300000040797.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040797.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040797/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040797 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC(=O)NCC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'C.ar', '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, 8, 1, 11, 8, 5, 5, 15, 15, 15, 14, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
122  conformations in input
total number of sets (complete confs): 122
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 10, 10, 34, 35, 35, 35, 83, 83, 83, 83, 1, 7, 7, 7, 7, 1, 1, 10, 34, 35, 83, 83, 7, 7] 122
rigid atoms, others: [6, 7, 8, 9, 10, 11, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 329
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040797 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC(=O)NCC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'C.ar', '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, 8, 1, 11, 8, 5, 5, 15, 15, 15, 14, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 12, 12, 12, 12, 48, 48, 78, 78, 78, 78, 123, 123, 123, 123, 12, 1, 1, 1, 1, 12, 12, 48, 78, 78, 123, 123, 1, 1] 123
rigid atoms, others: [1, 34, 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])
total number of confs: 423
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040797 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040797
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040797/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040797
Building REAL300000040798
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040798'
/scratch/stefan/7769621/working/building/REAL300000040798 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040798

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040798/0 /scratch/stefan/7769621/working/building/REAL300000040798 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 899)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/899
`/scratch/stefan/7769621/working/3D/899' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C2=CC=C(C=NNC(=O)NCC(F)(F)F)S2)=CC=C1)

`REAL300000040798.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040798.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040798/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040798 none O=C([O-])C1=CC(C2=CC=C(C=NNC(=O)NCC(F)(F)F)S2)=CC=C1 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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 8, 5, 5, 15, 15, 15, 14, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 9, 9, 25, 25, 25, 25, 105, 105, 105, 105, 1, 12, 12, 12, 12, 1, 1, 9, 25, 25, 105, 105, 12, 12, 12] 201
rigid atoms, others: [5, 6, 7, 8, 9, 10, 21, 26, 27] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 372
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040798 none O=C([O-])C1=CC(C2=CC=C(C=NNC(=O)NCC(F)(F)F)S2)=CC=C1 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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 8, 5, 5, 15, 15, 15, 14, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 12, 12, 12, 12, 53, 53, 119, 119, 119, 119, 201, 201, 201, 201, 12, 1, 1, 1, 1, 12, 12, 53, 119, 119, 201, 201, 1, 1, 1] 201
rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 35, 22, 23, 24, 25] set([0, 2, 7, 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: 742
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040798 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040798
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040798/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040798
Building REAL300000040799
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040799'
/scratch/stefan/7769621/working/building/REAL300000040799 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040799

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040799/0 /scratch/stefan/7769621/working/building/REAL300000040799 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 900)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/900
`/scratch/stefan/7769621/working/3D/900' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC(C(=O)[O-])=C(C=NNC(=O)NCC(F)(F)F)S1)

`REAL300000040799.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040799.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040799/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040799 none CCC1=CC(C(=O)[O-])=C(C=NNC(=O)NCC(F)(F)F)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 12, 12, 12, 35, 35, 35, 35, 1, 8, 8, 8, 7, 7, 1, 3, 11, 12, 35, 35] 61
rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 20, 26] set([0, 6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31])
total number of confs: 162
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040799 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040799
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040799/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040799
Building REAL300000040800
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040800'
/scratch/stefan/7769621/working/building/REAL300000040800 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040800

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040800/0 /scratch/stefan/7769621/working/building/REAL300000040800 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 901)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/901
`/scratch/stefan/7769621/working/3D/901' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=NNC(=O)NCC(F)(F)F)

`REAL300000040800.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040800.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040800/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040800 none COC1=CC=C(C(=O)[O-])C=C1C=NNC(=O)NCC(F)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
153  conformations in input
total number of sets (complete confs): 153
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 64, 65, 65, 65, 153, 153, 153, 153, 3, 3, 3, 1, 1, 1, 12, 64, 65, 153, 153] 153
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27] set([0, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31])
total number of confs: 547
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040800 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040800
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040800/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040800
Building REAL300000040801
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040801'
/scratch/stefan/7769621/working/building/REAL300000040801 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040801

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040801/0 /scratch/stefan/7769621/working/building/REAL300000040801 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 902)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/902
`/scratch/stefan/7769621/working/3D/902' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2SC=C(C=NNC(=O)NCC(F)(F)F)C2=C1)

`REAL300000040801.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040801.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040801/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040801 none O=C([O-])C1=CC=C2SC=C(C=NNC(=O)NCC(F)(F)F)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 14, 14, 14, 24, 24, 24, 24, 1, 1, 1, 1, 1, 4, 14, 14, 24, 24, 1] 24
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 31] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30])
total number of confs: 90
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040801 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040801
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040801/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040801
Building REAL300000040802
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040802'
/scratch/stefan/7769621/working/building/REAL300000040802 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040802

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040802/0 /scratch/stefan/7769621/working/building/REAL300000040802 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 903)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/903
`/scratch/stefan/7769621/working/3D/903' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2CCCC(=NNC(=O)NCC(F)(F)F)C2=C1)

`REAL300000040802.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040802.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040802/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040802 none O=C([O-])C1=CN=C2CCCC(=NNC(=O)NCC(F)(F)F)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 1, 1, 9, 9, 9, 9, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 15, 15, 1] 15
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 32, 2, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31])
total number of confs: 53
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040802 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040802
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040802/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040802
Building REAL300000040803
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040803'
/scratch/stefan/7769621/working/building/REAL300000040803 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040803

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040803/0 /scratch/stefan/7769621/working/building/REAL300000040803 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 904)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/904
`/scratch/stefan/7769621/working/3D/904' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(Br)C(C=NNC(=O)NCC(F)(F)F)=C1)

`REAL300000040803.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040803.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040803/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040803 none O=C([O-])C1=CC=C(Br)C(C=NNC(=O)NCC(F)(F)F)=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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 7, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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, 1, 1, 12, 12, 38, 38, 38, 38, 63, 63, 63, 63, 1, 1, 1, 12, 38, 38, 63, 63, 1] 63
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 28] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27])
total number of confs: 224
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040803 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040803
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040803/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040803
Building REAL300000040804
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040804'
/scratch/stefan/7769621/working/building/REAL300000040804 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040804

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040804/0 /scratch/stefan/7769621/working/building/REAL300000040804 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 905)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/905
`/scratch/stefan/7769621/working/3D/905' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C=NNC(=O)NCC(F)(F)F)C(C(=O)[O-])=C1)

`REAL300000040804.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040804.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040804/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040804 none CC1=CC=C(C=NNC(=O)NCC(F)(F)F)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 21, 21, 21, 21, 1, 1, 3, 3, 1, 2, 2, 2, 1, 1, 6, 11, 11, 21, 21, 1] 21
rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 20, 24, 25, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30])
total number of confs: 88
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040804 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040804
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040804/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040804
Building REAL300000040805
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040805'
/scratch/stefan/7769621/working/building/REAL300000040805 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040805

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040805/0 /scratch/stefan/7769621/working/building/REAL300000040805 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 906)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/906
`/scratch/stefan/7769621/working/3D/906' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)NCC(F)(F)F)=CC=C1C(=O)[O-])

`REAL300000040805.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040805.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040805/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040805 none COC1=CC(C=NNC(=O)NCC(F)(F)F)=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 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]
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: [3, 1, 1, 1, 1, 1, 12, 12, 55, 56, 56, 56, 139, 139, 139, 139, 1, 1, 1, 1, 3, 3, 4, 4, 4, 1, 12, 55, 56, 139, 139, 1, 1] 193
rigid atoms, others: [32, 1, 2, 3, 4, 5, 16, 17, 18, 19, 25, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30])
total number of confs: 504
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040805 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040805
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040805/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040805
Building REAL300000040806
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040806'
/scratch/stefan/7769621/working/building/REAL300000040806 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040806

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040806/0 /scratch/stefan/7769621/working/building/REAL300000040806 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 907)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/907
`/scratch/stefan/7769621/working/3D/907' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(F)=C(C=NNC(=O)NCC(F)(F)F)C(F)=C1)

`REAL300000040806.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040806.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040806/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040806 none O=C([O-])C1=CC(F)=C(C=NNC(=O)NCC(F)(F)F)C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 15, 1, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 24, 24, 24, 24, 33, 33, 33, 33, 1, 1, 1, 1, 8, 24, 24, 33, 33, 1] 33
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27])
total number of confs: 112
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040806 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040806
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040806/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040806
Building REAL300000040807
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040807'
/scratch/stefan/7769621/working/building/REAL300000040807 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040807

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040807/0 /scratch/stefan/7769621/working/building/REAL300000040807 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 908)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/908
`/scratch/stefan/7769621/working/3D/908' -> `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=NNC(=O)NCC(F)(F)F)=C1)

`REAL300000040807.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040807.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040807/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040807 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC(=O)NCC(F)(F)F)=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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 7, 6, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 36, 37, 37, 37, 60, 60, 60, 60, 1, 1, 2, 12, 36, 37, 60, 60, 1] 120
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28])
total number of confs: 219
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040807 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040807/1 /scratch/stefan/7769621/working/building/REAL300000040807 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 909)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/909
`/scratch/stefan/7769621/working/3D/909' -> `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=NNC(=O)NCC(F)(F)F)=C1)

`REAL300000040807.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040807.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040807/1/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: REAL300000040807 none O=C([O-])C1=CC(Br)=C([O-])C(C=NNC(=O)NCC(F)(F)F)=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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
16  conformations in input
total number of sets (complete confs): 16
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 16, 16, 16, 16, 1, 1, 6, 10, 10, 16, 16, 1] 16
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27])
total number of confs: 60
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040807 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040807
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040807/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040807/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040807
Building REAL300000040808
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040808'
/scratch/stefan/7769621/working/building/REAL300000040808 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040808

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040808/0 /scratch/stefan/7769621/working/building/REAL300000040808 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 910)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/910
`/scratch/stefan/7769621/working/3D/910' -> `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=NNC(=O)NCC(F)(F)F)C=C2)O1)

`REAL300000040808.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040808.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040808/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040808 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC(=O)NCC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.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, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 24, 25, 24, 24, 24, 9, 2, 1, 1, 1, 1, 1, 1, 9, 9, 23, 23, 23, 23, 79, 79, 79, 79, 1, 1, 24, 24, 24, 9, 9, 1, 1, 9, 23, 23, 79, 79, 1, 1] 201
rigid atoms, others: [32, 38, 39, 8, 9, 10, 11, 12, 13, 24, 25, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37])
total number of confs: 322
number of broken/clashed sets: 36
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040808 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC(=O)NCC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.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, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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
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, 8, 22, 24, 24, 22, 24, 65, 65, 97, 97, 97, 97, 201, 201, 201, 201, 24, 24, 1, 1, 1, 8, 8, 24, 24, 65, 97, 97, 201, 201, 24, 24] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 813
number of broken/clashed sets: 36
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040808 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040808
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040808/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040808
Building REAL300000040809
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040809'
/scratch/stefan/7769621/working/building/REAL300000040809 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040809

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040809/0 /scratch/stefan/7769621/working/building/REAL300000040809 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 911)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/911
`/scratch/stefan/7769621/working/3D/911' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC=CC=C2C(C=NNC(=O)NCC(F)(F)F)=C1O)

`REAL300000040809.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040809.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040809/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040809 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC(=O)NCC(F)(F)F)=C1O 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.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', '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, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
132  conformations in input
total number of sets (complete confs): 132
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 26, 26, 26, 26, 66, 66, 66, 66, 1, 1, 1, 1, 1, 1, 1, 10, 26, 26, 66, 66, 2] 132
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29] set([0, 32, 2, 34, 35, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31])
total number of confs: 247
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040809 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040809
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040809/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040809
Building REAL300000040810
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040810'
/scratch/stefan/7769621/working/building/REAL300000040810 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040810

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040810/0 /scratch/stefan/7769621/working/building/REAL300000040810 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 912)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/912
`/scratch/stefan/7769621/working/3D/912' -> `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=NNC(=O)NCC(F)(F)F)C=C2)=C1)

`REAL300000040810.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040810.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040810/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040810 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC(=O)NCC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 5, 13, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 40, 41, 41, 41, 89, 89, 89, 89, 1, 1, 3, 5, 5, 3, 3, 3, 1, 1, 10, 40, 41, 89, 89, 1, 1, 3] 201
rigid atoms, others: [32, 33, 39, 8, 9, 10, 11, 12, 13, 40, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 41])
total number of confs: 362
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040810 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC(=O)NCC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 12, 13, 71, 66, 71, 71, 121, 121, 121, 121, 3, 3, 1, 2, 2, 1, 1, 1, 3, 3, 12, 67, 71, 121, 121, 3, 3, 1] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 41, 26, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 443
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040810 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040810
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040810/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040810
Building REAL300000040811
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040811'
/scratch/stefan/7769621/working/building/REAL300000040811 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040811

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040811/0 /scratch/stefan/7769621/working/building/REAL300000040811 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 913)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/913
`/scratch/stefan/7769621/working/3D/913' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NNC(=O)NCC(F)(F)F)SC(Cl)=C1)

`REAL300000040811.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040811.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040811/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040811 none O=C([O-])C1=C(C=NNC(=O)NCC(F)(F)F)SC(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 14, 1, 16, 1, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 3, 3, 11, 12, 12, 12, 30, 30, 30, 30, 1, 1, 1, 1, 3, 11, 12, 30, 30, 1] 30
rigid atoms, others: [1, 3, 4, 5, 16, 17, 18, 19, 25] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24])
total number of confs: 114
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040811 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040811
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040811/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040811
Building REAL300000040812
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040812'
/scratch/stefan/7769621/working/building/REAL300000040812 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040812

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040812/0 /scratch/stefan/7769621/working/building/REAL300000040812 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 914)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/914
`/scratch/stefan/7769621/working/3D/914' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC(C=NNC(=O)NCC(F)(F)F)=CC=C1OCC(=O)[O-])

`REAL300000040812.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040812.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040812/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040812 none CCOC1=CC(C=NNC(=O)NCC(F)(F)F)=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.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 29, 29, 29, 29, 1, 1, 1, 1, 9, 38, 65, 65, 19, 19, 19, 19, 19, 1, 5, 7, 8, 29, 29, 1, 1, 38, 38] 201
rigid atoms, others: [2, 3, 4, 5, 6, 17, 18, 19, 20, 36, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 38, 39])
total number of confs: 356
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040812 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040812
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040812/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040812
Building REAL300000040813
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040813'
/scratch/stefan/7769621/working/building/REAL300000040813 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040813

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040813/0 /scratch/stefan/7769621/working/building/REAL300000040813 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 915)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/915
`/scratch/stefan/7769621/working/3D/915' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC(=O)NCC(F)(F)F)

`REAL300000040813.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040813.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040813/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040813 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC(=O)NCC(F)(F)F 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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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, 8, 1, 11, 8, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [21, 13, 21, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 25, 25, 46, 46, 46, 46, 82, 82, 82, 82, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 25, 46, 46, 82, 82] 82
rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39])
total number of confs: 314
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040813 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC(=O)NCC(F)(F)F 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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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, 8, 1, 11, 8, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 1, 4, 4, 8, 8, 8, 8, 26, 26, 26, 26, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 4, 8, 8, 26, 26] 82
rigid atoms, others: [1, 34, 3, 4, 5, 6, 12, 13, 14] set([0, 2, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39])
total number of confs: 124
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040813 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040813
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040813/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040813
Building REAL300000040814
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040814'
/scratch/stefan/7769621/working/building/REAL300000040814 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040814

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040814/0 /scratch/stefan/7769621/working/building/REAL300000040814 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 916)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/916
`/scratch/stefan/7769621/working/3D/916' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C)C(C=NNC(=O)NCC(F)(F)F)=C1C(=O)[O-])

`REAL300000040814.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040814.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040814/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040814 none COC1=CC=C(C)C(C=NNC(=O)NCC(F)(F)F)=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.am', 'C.2', 'O.2', 'N.am', 'C.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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 18, 18, 18, 56, 56, 56, 56, 1, 1, 3, 3, 4, 4, 4, 1, 1, 2, 2, 2, 5, 18, 18, 56, 56] 78
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 26, 27] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 211
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040814 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040814
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040814/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040814
Building REAL300000040815
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040815'
/scratch/stefan/7769621/working/building/REAL300000040815 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040815

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040815/0 /scratch/stefan/7769621/working/building/REAL300000040815 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 917)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/917
`/scratch/stefan/7769621/working/3D/917' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C2=CC=C(F)C=C2C(C=NNC(=O)NCC(F)(F)F)=C1C(=O)[O-])

`REAL300000040815.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040815.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040815/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040815 none CN1C2=CC=C(F)C=C2C(C=NNC(=O)NCC(F)(F)F)=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.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 24, 24, 24, 24, 1, 1, 3, 3, 2, 2, 2, 1, 1, 1, 4, 9, 9, 24, 24] 24
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 28, 29, 30] set([32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 31])
total number of confs: 103
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040815 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040815
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040815/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040815
Building REAL300000040816
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040816'
/scratch/stefan/7769621/working/building/REAL300000040816 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040816

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040816/0 /scratch/stefan/7769621/working/building/REAL300000040816 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 918)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/918
`/scratch/stefan/7769621/working/3D/918' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NCC(F)(F)F)C1=C(C(=O)[O-])C2=CC=CC=C2S1)

`REAL300000040816.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040816.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040816/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040816 none CC(=NNC(=O)NCC(F)(F)F)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [6, 1, 6, 6, 19, 19, 19, 19, 46, 46, 46, 46, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 46, 46, 1, 1, 1, 1] 46
rigid atoms, others: [32, 1, 34, 33, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 179
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040816 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040816
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040816/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040816
Building REAL300000040817
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040817'
/scratch/stefan/7769621/working/building/REAL300000040817 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040817

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040817/0 /scratch/stefan/7769621/working/building/REAL300000040817 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 919)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/919
`/scratch/stefan/7769621/working/3D/919' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCC1=CC=C(C=NNC(=O)NCC(F)(F)F)O1)

`REAL300000040817.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040817.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040817/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040817 none O=C([O-])CCC1=CC=C(C=NNC(=O)NCC(F)(F)F)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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: [34, 21, 26, 9, 1, 1, 1, 1, 1, 1, 6, 6, 22, 23, 23, 23, 83, 83, 83, 83, 1, 21, 21, 9, 9, 1, 1, 6, 22, 23, 83, 83] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 20, 25, 26] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 27, 28, 29, 30, 31])
total number of confs: 403
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040817 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040817
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040817/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040817
Building REAL300000040818
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040818'
/scratch/stefan/7769621/working/building/REAL300000040818 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040818

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040818/0 /scratch/stefan/7769621/working/building/REAL300000040818 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 920)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/920
`/scratch/stefan/7769621/working/3D/920' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NNC(=O)NCC(F)(F)F)SC(Br)=C1)

`REAL300000040818.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040818.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040818/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040818 none O=C([O-])C1=C(C=NNC(=O)NCC(F)(F)F)SC(Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 14, 1, 17, 1, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 3, 3, 11, 12, 12, 12, 30, 30, 30, 30, 1, 1, 1, 1, 3, 11, 12, 30, 30, 1] 30
rigid atoms, others: [1, 3, 4, 5, 16, 17, 18, 19, 25] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24])
total number of confs: 114
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040818 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040818
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040818/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040818
Building REAL300000040819
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040819'
/scratch/stefan/7769621/working/building/REAL300000040819 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040819

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040819/0 /scratch/stefan/7769621/working/building/REAL300000040819 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 921)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/921
`/scratch/stefan/7769621/working/3D/921' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C2NC=C(C=NNC(=O)NCC(F)(F)F)C2=CC=C1)

`REAL300000040819.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040819.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040819/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040819 none O=C([O-])C1=C2NC=C(C=NNC(=O)NCC(F)(F)F)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 10, 36, 37, 37, 37, 61, 61, 61, 61, 1, 1, 1, 1, 1, 1, 10, 36, 37, 61, 61, 1, 1, 1] 61
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29])
total number of confs: 215
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040819 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040819
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040819/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040819
Building REAL300000040820
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040820'
/scratch/stefan/7769621/working/building/REAL300000040820 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040820

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040820/0 /scratch/stefan/7769621/working/building/REAL300000040820 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 922)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/922
`/scratch/stefan/7769621/working/3D/922' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)NCC(F)(F)F)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1)

`REAL300000040820.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040820.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040820/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040820 none CC(=NNC(=O)NCC(F)(F)F)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 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: [3, 1, 3, 3, 9, 9, 9, 9, 17, 17, 17, 17, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 17, 17, 1, 1, 1, 1, 1] 17
rigid atoms, others: [32, 1, 34, 35, 36, 33, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 69
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040820 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040820
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040820/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040820
Building REAL300000040821
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040821'
/scratch/stefan/7769621/working/building/REAL300000040821 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040821

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040821/0 /scratch/stefan/7769621/working/building/REAL300000040821 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 923)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/923
`/scratch/stefan/7769621/working/3D/923' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC(C=NNC(=O)NCC(F)(F)F)=CC=C2O1)

`REAL300000040821.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040821.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040821/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040821 none O=C([O-])C1=CC2=CC(C=NNC(=O)NCC(F)(F)F)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 29, 30, 30, 30, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 11, 29, 30, 47, 47, 1, 1] 47
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29])
total number of confs: 165
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040821 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040821
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040821/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040821
Building REAL300000040822
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040822'
/scratch/stefan/7769621/working/building/REAL300000040822 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040822

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040822/0 /scratch/stefan/7769621/working/building/REAL300000040822 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 924)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/924
`/scratch/stefan/7769621/working/3D/924' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2C(C=NNC(=O)NCC(F)(F)F)=CC=CN12)

`REAL300000040822.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040822.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040822/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040822 none O=C([O-])C1=CN=C2C(C=NNC(=O)NCC(F)(F)F)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 8, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 17, 18, 18, 18, 26, 26, 26, 26, 1, 1, 1, 1, 1, 5, 17, 18, 26, 26, 1, 1, 1] 26
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 29, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28])
total number of confs: 98
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040822 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040822
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040822/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040822
Building REAL300000040823
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040823'
/scratch/stefan/7769621/working/building/REAL300000040823 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040823

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040823/0 /scratch/stefan/7769621/working/building/REAL300000040823 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 925)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/925
`/scratch/stefan/7769621/working/3D/925' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(F)C=CC=C1C=NNC(=O)NCC(F)(F)F)

`REAL300000040823.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040823.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040823/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040823 none O=C([O-])C1=C(F)C=CC=C1C=NNC(=O)NCC(F)(F)F NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 18, 18, 18, 18, 1, 1, 1, 4, 8, 8, 18, 18] 18
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28])
total number of confs: 74
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040823 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040823
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040823/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040823
Building REAL300000040824
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040824'
/scratch/stefan/7769621/working/building/REAL300000040824 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040824

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040824/0 /scratch/stefan/7769621/working/building/REAL300000040824 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 926)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/926
`/scratch/stefan/7769621/working/3D/926' -> `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=NNC(=O)NCC(F)(F)F)O1)

`REAL300000040824.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040824.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040824/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040824 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC(=O)NCC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'O.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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
128  conformations in input
total number of sets (complete confs): 128
using faster count positions algorithm for large data
unique positions, atoms: [49, 49, 49, 49, 49, 49, 20, 9, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 28, 28, 28, 28, 49, 49, 49, 20, 20, 1, 1, 1, 1, 5, 7, 7, 28, 28] 128
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, 38, 39])
total number of confs: 190
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040824 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC(=O)NCC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'O.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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
128  conformations in input
total number of sets (complete confs): 128
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 29, 49, 49, 49, 49, 49, 49, 59, 59, 61, 61, 61, 61, 128, 128, 128, 128, 1, 1, 1, 8, 8, 49, 49, 49, 49, 59, 61, 61, 128, 128] 128
rigid atoms, others: [1, 3, 4, 5, 6, 7, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 452
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040824 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040824
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040824/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040824
Building REAL300000040825
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040825'
/scratch/stefan/7769621/working/building/REAL300000040825 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040825

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040825/0 /scratch/stefan/7769621/working/building/REAL300000040825 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 927)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/927
`/scratch/stefan/7769621/working/3D/927' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Br)C=CC=C1C=NNC(=O)NCC(F)(F)F)

`REAL300000040825.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040825.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040825/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040825 none O=C([O-])C1=C(Br)C=CC=C1C=NNC(=O)NCC(F)(F)F 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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 12, 12, 12, 12, 1, 1, 1, 4, 8, 8, 12, 12] 12
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28])
total number of confs: 48
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040825 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040825
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040825/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040825
Building REAL300000040826
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040826'
/scratch/stefan/7769621/working/building/REAL300000040826 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040826

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040826/0 /scratch/stefan/7769621/working/building/REAL300000040826 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 928)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/928
`/scratch/stefan/7769621/working/3D/928' -> `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=NNC(=O)NCC(F)(F)F)

`REAL300000040826.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040826.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040826/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040826 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NNC(=O)NCC(F)(F)F 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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 7, 7, 22, 22, 22, 22, 93, 93, 93, 93, 2, 3, 3, 1, 3, 3, 3, 1, 1, 7, 22, 22, 93, 93] 110
rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 34, 15, 16, 35, 30] set([0, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 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
/scratch/stefan/7769621/working/building/REAL300000040826 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040826
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040826/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040826
Building REAL300000040827
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040827'
/scratch/stefan/7769621/working/building/REAL300000040827 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040827

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040827/0 /scratch/stefan/7769621/working/building/REAL300000040827 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 929)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/929
`/scratch/stefan/7769621/working/3D/929' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NNC(=O)NCC(F)(F)F)C2=C(C=C1)OCO2)

`REAL300000040827.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040827.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040827/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040827 none O=C([O-])C1=C(C=NNC(=O)NCC(F)(F)F)C2=C(C=C1)OCO2 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 12, 5, 12, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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, 1, 1, 1, 6, 6, 15, 15, 15, 15, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 1, 6, 15, 15, 33, 33, 1, 1, 1, 1] 33
rigid atoms, others: [1, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27])
total number of confs: 131
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040827 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040827
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040827/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040827
Building REAL300000040828
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040828'
/scratch/stefan/7769621/working/building/REAL300000040828 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040828

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040828/0 /scratch/stefan/7769621/working/building/REAL300000040828 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 930)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/930
`/scratch/stefan/7769621/working/3D/930' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=CC=C(C(=O)[O-])C(C=NNC(=O)NCC(F)(F)F)=C1)

`REAL300000040828.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040828.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040828/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040828 none N#CC1=CC=C(C(=O)[O-])C(C=NNC(=O)NCC(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 7, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 6, 6, 12, 12, 12, 12, 25, 25, 25, 25, 1, 1, 1, 6, 12, 12, 25, 25, 1] 25
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 21, 22, 23, 29] set([7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28])
total number of confs: 99
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040828 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040828
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040828/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040828
Building REAL300000040829
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040829'
/scratch/stefan/7769621/working/building/REAL300000040829 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040829

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040829/0 /scratch/stefan/7769621/working/building/REAL300000040829 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 931)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/931
`/scratch/stefan/7769621/working/3D/931' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC(=O)NCC(F)(F)F)C=C1Cl)

`REAL300000040829.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040829.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040829/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040829 none O=C([O-])COC1=CC=C(C=NNC(=O)NCC(F)(F)F)C=C1Cl 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.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 11, 8, 5, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [59, 35, 59, 10, 1, 1, 1, 1, 1, 1, 6, 6, 18, 19, 19, 19, 71, 71, 71, 71, 1, 1, 1, 35, 35, 1, 1, 6, 18, 19, 71, 71, 1] 201
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 20, 21, 22, 25, 26] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 27, 28, 29, 30, 31])
total number of confs: 441
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040829 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040829
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040829/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040829
Building REAL300000040830
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040830'
/scratch/stefan/7769621/working/building/REAL300000040830 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040830

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040830/0 /scratch/stefan/7769621/working/building/REAL300000040830 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 932)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/932
`/scratch/stefan/7769621/working/3D/932' -> `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=NNC(=O)NCC(F)(F)F)C=C1)

`REAL300000040830.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040830.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040830/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040830 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC(=O)NCC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 15, 41, 41, 41, 41, 1, 1, 9, 9, 5, 1, 1, 6, 14, 15, 41, 41, 1, 1] 77
rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 36, 28, 29] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34])
total number of confs: 184
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040830 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040830
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040830/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040830
Building REAL300000040831
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040831'
/scratch/stefan/7769621/working/building/REAL300000040831 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040831

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040831/0 /scratch/stefan/7769621/working/building/REAL300000040831 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 933)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/933
`/scratch/stefan/7769621/working/3D/933' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NSC(C=NNC(=O)NCC(F)(F)F)=C1C(=O)[O-])

`REAL300000040831.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040831.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040831/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040831 none CC1=NSC(C=NNC(=O)NCC(F)(F)F)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 12, 12, 28, 28, 28, 28, 1, 1, 2, 2, 2, 2, 2, 4, 11, 12, 28, 28] 28
rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 110
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040831 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040831
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040831/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040831
Building REAL300000040832
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040832'
/scratch/stefan/7769621/working/building/REAL300000040832 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040832

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040832/0 /scratch/stefan/7769621/working/building/REAL300000040832 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 934)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/934
`/scratch/stefan/7769621/working/3D/934' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=C(C=NNC(=O)NCC(F)(F)F)C(F)=CC=C2S1)

`REAL300000040832.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040832.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040832/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040832 none O=C([O-])C1=CC2=C(C=NNC(=O)NCC(F)(F)F)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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 1, 15, 1, 1, 1, 14, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 11, 11, 30, 31, 31, 31, 52, 52, 52, 52, 1, 1, 1, 1, 1, 1, 1, 11, 30, 31, 52, 52, 1, 1] 52
rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 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/7769621/working/building/REAL300000040832 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040832
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040832/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040832
Building REAL300000040833
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040833'
/scratch/stefan/7769621/working/building/REAL300000040833 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040833

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040833/0 /scratch/stefan/7769621/working/building/REAL300000040833 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 935)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/935
`/scratch/stefan/7769621/working/3D/935' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=NNC(=O)NCC(F)(F)F)

`REAL300000040833.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040833.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040833/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040833 none COC1=CC(C(=O)[O-])=CC=C1C=NNC(=O)NCC(F)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 10, 10, 23, 23, 23, 23, 55, 55, 55, 55, 3, 3, 3, 1, 1, 1, 10, 23, 23, 55, 55] 55
rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 11, 25, 26, 27] set([0, 32, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31])
total number of confs: 201
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040833 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040833
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040833/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040833
Building REAL300000040834
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040834'
/scratch/stefan/7769621/working/building/REAL300000040834 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040834

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040834/0 /scratch/stefan/7769621/working/building/REAL300000040834 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 936)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/936
`/scratch/stefan/7769621/working/3D/936' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC(=O)NCC(F)(F)F)=N2)C1)

`REAL300000040834.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040834.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040834/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040834 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC(=O)NCC(F)(F)F)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [23, 12, 23, 12, 12, 12, 1, 12, 1, 1, 1, 1, 1, 4, 4, 21, 21, 21, 21, 57, 57, 57, 57, 1, 12, 12, 12, 1, 1, 4, 21, 21, 57, 57, 12, 12] 140
rigid atoms, others: [6, 8, 9, 10, 11, 12, 23, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 272
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040834 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC(=O)NCC(F)(F)F)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 30, 30, 79, 79, 79, 79, 140, 140, 140, 140, 12, 1, 1, 1, 12, 12, 30, 79, 79, 140, 140, 1, 1] 140
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 35, 24, 25, 26] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 506
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040834 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040834
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040834/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040834
Building REAL300000040835
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040835'
/scratch/stefan/7769621/working/building/REAL300000040835 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040835

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040835/0 /scratch/stefan/7769621/working/building/REAL300000040835 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 937)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/937
`/scratch/stefan/7769621/working/3D/937' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=CC=C1C=NNC1=C2N=CN=C2N=C[N-]1)

`REAL300000040835.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040835.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040835/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040835 none O=C([O-])COC1=CC=CC=C1C=NNC1=C2N=CN=C2N=C[N-]1 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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', '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, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
150  conformations in input
total number of sets (complete confs): 150
using faster count positions algorithm for large data
unique positions, atoms: [150, 150, 150, 128, 66, 66, 66, 44, 66, 66, 44, 44, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 150, 150, 66, 66, 66, 66, 44, 9, 1, 1] 150
rigid atoms, others: [32, 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: 424
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040835 none O=C([O-])COC1=CC=CC=C1C=NNC1=C2N=CN=C2N=C[N-]1 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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', '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, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
150  conformations in input
total number of sets (complete confs): 150
using faster count positions algorithm for large data
unique positions, atoms: [56, 32, 56, 10, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 20, 66, 66, 66, 66, 66, 66, 66, 66, 32, 32, 1, 1, 1, 1, 4, 20, 66, 66] 150
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27, 28] set([0, 1, 2, 3, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31])
total number of confs: 285
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040835 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040835/1 /scratch/stefan/7769621/working/building/REAL300000040835 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 938)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/938
`/scratch/stefan/7769621/working/3D/938' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=CC=C1CN=NC1=C2N=CNC2=NC=N1)

`REAL300000040835.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040835.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040835/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040835 none O=C([O-])COC1=CC=CC=C1CN=NC1=C2N=CNC2=NC=N1 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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 131, 53, 53, 53, 27, 53, 53, 15, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 53, 53, 53, 53, 14, 15, 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: 680
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040835 none O=C([O-])COC1=CC=CC=C1CN=NC1=C2N=CNC2=NC=N1 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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [54, 30, 54, 7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 39, 40, 53, 53, 53, 53, 53, 53, 53, 53, 30, 30, 1, 1, 1, 1, 6, 6, 53, 53, 53] 201
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: 262
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040835 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040835
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040835/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040835/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040835
Building REAL300000040836
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040836'
/scratch/stefan/7769621/working/building/REAL300000040836 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040836

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040836/0 /scratch/stefan/7769621/working/building/REAL300000040836 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 939)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/939
`/scratch/stefan/7769621/working/3D/939' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2N=CN=C2NC=N1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1)

`REAL300000040836.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040836.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040836/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040836 none CC(=NNC1=C2N=CN=C2NC=N1)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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 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]
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: [26, 1, 26, 26, 127, 171, 171, 171, 171, 171, 171, 171, 171, 1, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 26, 26, 26, 120, 171, 171, 171, 12, 12, 1, 1, 12, 12] 171
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: 395
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: REAL300000040836 none CC(=NNC1=C2N=CN=C2NC=N1)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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 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]
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: [6, 1, 6, 6, 35, 105, 105, 105, 105, 105, 105, 105, 105, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 6, 6, 6, 35, 105, 105, 105, 1, 1, 12, 12, 1, 1] 171
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: 188
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040836 none CC(=NNC1=C2N=CN=C2NC=N1)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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 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]
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: [45, 45, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 105, 105, 46, 59, 171, 171, 171, 171, 171, 171, 171, 105, 105, 46, 46, 46, 10, 1, 1, 1, 105, 105, 171, 171, 105, 105] 171
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: 468
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040836 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040836
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040836/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040836
Building REAL300000040837
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040837'
/scratch/stefan/7769621/working/building/REAL300000040837 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040837

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040837/0 /scratch/stefan/7769621/working/building/REAL300000040837 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 940)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/940
`/scratch/stefan/7769621/working/3D/940' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=C3N=CN=C3N=C[N-]2)=CC=C1OCC(=O)[O-])

`REAL300000040837.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040837.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040837/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040837 none COC1=CC(C=NNC2=C3N=CN=C3N=C[N-]2)=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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 12, 5, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 3, 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: [99, 55, 55, 55, 22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 54, 54, 156, 201, 201, 201, 99, 99, 99, 55, 22, 6, 1, 1, 55, 55, 201, 201] 201
rigid atoms, others: [32, 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, 33, 34, 35, 36])
total number of confs: 536
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040837 none COC1=CC(C=NNC2=C3N=CN=C3N=C[N-]2)=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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 12, 5, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 3, 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: [3, 1, 1, 1, 1, 1, 7, 7, 33, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1, 9, 27, 56, 56, 3, 3, 3, 1, 7, 33, 55, 55, 1, 1, 27, 27] 201
rigid atoms, others: [1, 2, 3, 4, 5, 33, 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, 35, 36])
total number of confs: 297
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040837 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040837
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040837/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040837
Building REAL300000040838
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040838'
/scratch/stefan/7769621/working/building/REAL300000040838 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040838

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040838/0 /scratch/stefan/7769621/working/building/REAL300000040838 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 941)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/941
`/scratch/stefan/7769621/working/3D/941' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)C=C1)

`REAL300000040838.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040838.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040838/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040838 none O=C([O-])COC1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', '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, 8, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 180, 96, 93, 135, 135, 57, 57, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 135, 135, 201, 201, 135, 135, 57, 10, 1, 1, 135, 135] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 21, 22, 23, 24, 25, 26, 27, 28, 31])
total number of confs: 578
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040838 none O=C([O-])COC1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', '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, 8, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 12, 23, 3, 1, 1, 1, 1, 1, 1, 13, 13, 51, 135, 135, 135, 135, 135, 135, 135, 135, 1, 1, 12, 12, 1, 1, 13, 51, 135, 135, 1, 1] 201
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 21, 22, 25, 26, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30])
total number of confs: 307
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040838 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040838/1 /scratch/stefan/7769621/working/building/REAL300000040838 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 942)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/942
`/scratch/stefan/7769621/working/3D/942' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(CN=NC2=C3N=CNC3=NC=N2)C=C1)

`REAL300000040838.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040838.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040838/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040838 none O=C([O-])COC1=CC=C(CN=NC2=C3N=CNC3=NC=N2)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 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, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 146, 88, 25, 89, 89, 20, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 89, 89, 201, 201, 89, 89, 20, 20, 1, 1, 1, 89, 89] 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: 763
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040838 none O=C([O-])COC1=CC=C(CN=NC2=C3N=CNC3=NC=N2)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.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, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 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, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 9, 20, 3, 1, 1, 1, 1, 1, 1, 8, 58, 58, 89, 89, 89, 89, 89, 89, 89, 89, 1, 1, 9, 9, 1, 1, 8, 8, 89, 89, 89, 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: 201
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040838 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040838
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040838/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040838/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040838
Building REAL300000040839
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040839'
/scratch/stefan/7769621/working/building/REAL300000040839 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040839

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040839/0 /scratch/stefan/7769621/working/building/REAL300000040839 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 943)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/943
`/scratch/stefan/7769621/working/3D/943' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2N=CN=C2NC=N1)C1=CC=CC(OCC(=O)[O-])=C1)

`REAL300000040839.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040839.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040839/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040839 none CC(=NNC1=C2N=CN=C2NC=N1)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 38, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 1, 7, 23, 39, 39, 1, 11, 11, 11, 38, 65, 65, 65, 1, 1, 1, 23, 23, 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: 261
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040839 none CC(=NNC1=C2N=CN=C2NC=N1)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 65, 65, 65, 65, 65, 151, 201, 201, 201, 65, 21, 21, 21, 6, 1, 1, 1, 65, 65, 65, 201, 201, 65] 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: 486
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040839 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040839
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040839/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040839
Building REAL300000040840
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040840'
/scratch/stefan/7769621/working/building/REAL300000040840 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040840

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040840/0 /scratch/stefan/7769621/working/building/REAL300000040840 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 944)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/944
`/scratch/stefan/7769621/working/3D/944' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2N=CN=C2N=C[N-]1)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1)

`REAL300000040840.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040840.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040840/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040840 none CC(=NNC1=C2N=CN=C2N=C[N-]1)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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 2, 2, 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: [6, 1, 6, 6, 31, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 2, 2, 2, 9, 16, 16, 16, 1, 1, 6, 6, 6, 31, 67, 67, 1, 1, 9, 16, 16, 1, 1] 159
rigid atoms, others: [1, 34, 38, 33, 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, 35, 36, 37])
total number of confs: 195
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040840 none CC(=NNC1=C2N=CN=C2N=C[N-]1)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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 2, 2, 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: [25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 67, 67, 25, 43, 113, 113, 113, 157, 159, 159, 159, 67, 67, 25, 25, 25, 7, 1, 1, 67, 67, 157, 159, 159, 67, 67] 159
rigid atoms, others: [32, 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, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 709
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040840 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040840
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040840/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040840
Building REAL300000040841
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040841'
/scratch/stefan/7769621/working/building/REAL300000040841 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040841

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040841/0 /scratch/stefan/7769621/working/building/REAL300000040841 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 945)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/945
`/scratch/stefan/7769621/working/3D/945' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2N=CN=C2NC=N1)C1=CC=C(CC(=O)[O-])C=C1)

`REAL300000040841.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040841.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040841/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040841 none CC(=NNC1=C2N=CN=C2NC=N1)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 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, 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: [6, 1, 6, 6, 31, 62, 62, 62, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 6, 6, 6, 31, 62, 62, 62, 1, 1, 2, 2, 1, 1] 83
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: 146
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040841 none CC(=NNC1=C2N=CN=C2NC=N1)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 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, 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: [38, 38, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 62, 62, 48, 62, 83, 83, 83, 62, 62, 39, 39, 39, 10, 1, 1, 1, 62, 62, 83, 83, 62, 62] 83
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: 295
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040841 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040841
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040841/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040841
Building REAL300000040842
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040842'
/scratch/stefan/7769621/working/building/REAL300000040842 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040842

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040842/0 /scratch/stefan/7769621/working/building/REAL300000040842 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 946)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/946
`/scratch/stefan/7769621/working/3D/946' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])OC2=C1C(=NNC1=C3N=CN=C3NC=N1)CCC2)

`REAL300000040842.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040842.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040842/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040842 none CC1=C(C(=O)[O-])OC2=C1C(=NNC1=C3N=CN=C3NC=N1)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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 5, 5, 5, 7, 7, 7, 6, 7, 6, 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, 4, 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, 34, 34, 34, 35, 35, 34, 34, 34, 34, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 35, 35, 35, 10, 1, 1, 1, 34, 34, 34, 34, 34, 34] 35
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36])
total number of confs: 64
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040842 none CC1=C(C(=O)[O-])OC2=C1C(=NNC1=C3N=CN=C3NC=N1)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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 5, 5, 5, 7, 7, 7, 6, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 8, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 2, 2, 2, 8, 34, 34, 34, 1, 1, 1, 1, 1, 1] 35
rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 11, 34, 35, 21, 22, 23, 36, 31] set([4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 61
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040842 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040842
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040842/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040842
Building REAL300000040843
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040843'
/scratch/stefan/7769621/working/building/REAL300000040843 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040843

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040843/0 /scratch/stefan/7769621/working/building/REAL300000040843 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 947)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/947
`/scratch/stefan/7769621/working/3D/947' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)C=C1)

`REAL300000040843.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040843.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040843/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040843 none O=C([O-])CCOC1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 197, 181, 158, 77, 73, 96, 96, 39, 39, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 96, 96, 201, 201, 181, 181, 96, 96, 39, 6, 1, 1, 96, 96] 201
rigid atoms, others: [32, 33, 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, 34, 35])
total number of confs: 577
number of broken/clashed sets: 33
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040843 none O=C([O-])CCOC1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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]
0  hydrogens 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, 22, 12, 3, 1, 1, 1, 1, 1, 1, 11, 11, 43, 96, 96, 96, 96, 96, 96, 96, 96, 1, 1, 18, 18, 12, 12, 1, 1, 11, 43, 96, 96, 1, 1] 201
rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 22, 23, 28, 29] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 30, 31, 32, 33])
total number of confs: 268
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040843 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040843/1 /scratch/stefan/7769621/working/building/REAL300000040843 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 948)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/948
`/scratch/stefan/7769621/working/3D/948' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=C(CN=NC2=C3N=CNC3=NC=N2)C=C1)

`REAL300000040843.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040843.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040843/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040843 none O=C([O-])CCOC1=CC=C(CN=NC2=C3N=CNC3=NC=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 200, 200, 98, 28, 99, 99, 22, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 99, 99, 200, 200, 201, 200, 99, 99, 22, 22, 1, 1, 1, 99, 99] 201
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36])
total number of confs: 549
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040843 none O=C([O-])CCOC1=CC=C(CN=NC2=C3N=CNC3=NC=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 5, 9, 5, 3, 1, 1, 1, 1, 1, 1, 8, 62, 62, 99, 99, 99, 99, 99, 99, 99, 99, 1, 1, 5, 5, 5, 5, 1, 1, 8, 8, 99, 99, 99, 1, 1] 201
rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 22, 23, 28, 29] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 30, 31, 32, 33, 34])
total number of confs: 188
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040843 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040843
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040843/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040843/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040843
Building REAL300000040844
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040844'
/scratch/stefan/7769621/working/building/REAL300000040844 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040844

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040844/0 /scratch/stefan/7769621/working/building/REAL300000040844 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 949)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/949
`/scratch/stefan/7769621/working/3D/949' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(Br)C=C1C=NNC1=C2N=CN=C2N=C[N-]1)

`REAL300000040844.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040844.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040844/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040844 none O=C([O-])COC1=CC=C(Br)C=C1C=NNC1=C2N=CN=C2N=C[N-]1 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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 150, 72, 72, 72, 72, 72, 72, 72, 48, 48, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 176, 176, 72, 72, 72, 48, 9, 1, 1] 176
rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 377
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040844 none O=C([O-])COC1=CC=C(Br)C=C1C=NNC1=C2N=CN=C2N=C[N-]1 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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
176  conformations in input
total number of sets (complete confs): 176
using faster count positions algorithm for large data
unique positions, atoms: [59, 35, 59, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 22, 72, 72, 72, 72, 72, 72, 72, 72, 35, 35, 1, 1, 1, 4, 22, 72, 72] 176
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28] set([0, 1, 2, 3, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31])
total number of confs: 308
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040844 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040844
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040844/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040844
Building REAL300000040845
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040845'
/scratch/stefan/7769621/working/building/REAL300000040845 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040845

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040845/0 /scratch/stefan/7769621/working/building/REAL300000040845 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 950)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/950
`/scratch/stefan/7769621/working/3D/950' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=CC(C=NNC2=C3N=CN=C3N=C[N-]2)=C1)C(=O)[O-])

`REAL300000040845.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040845.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040845/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040845 none CC(OC1=CC=CC(C=NNC2=C3N=CN=C3N=C[N-]2)=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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 162, 67, 66, 66, 66, 66, 39, 39, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 201, 201, 201, 201, 201, 201, 201, 66, 66, 66, 39, 6, 1, 1, 67] 201
rigid atoms, others: [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, 32, 35])
total number of confs: 452
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040845 none CC(OC1=CC=CC(C=NNC2=C3N=CN=C3N=C[N-]2)=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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 30, 67, 67, 67, 67, 67, 67, 67, 67, 1, 30, 43, 43, 30, 30, 30, 30, 1, 1, 1, 6, 29, 67, 67, 1] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 35, 20, 28, 29, 30] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 269
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040845 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040845/1 /scratch/stefan/7769621/working/building/REAL300000040845 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 951)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/951
`/scratch/stefan/7769621/working/3D/951' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=CC(CN=NC2=C3N=CNC3=NC=N2)=C1)C(=O)[O-])

`REAL300000040845.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040845.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040845/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040845 none CC(OC1=CC=CC(CN=NC2=C3N=CNC3=NC=N2)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.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, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 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: [201, 170, 52, 52, 52, 52, 52, 11, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 201, 201, 201, 201, 201, 201, 201, 52, 52, 52, 10, 11, 1, 1, 1, 52] 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])
total number of confs: 424
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040845 none CC(OC1=CC=CC(CN=NC2=C3N=CNC3=NC=N2)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.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, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 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: [23, 9, 1, 1, 1, 1, 1, 1, 1, 8, 51, 51, 52, 52, 52, 52, 52, 52, 52, 52, 1, 23, 29, 29, 23, 23, 23, 23, 1, 1, 1, 8, 8, 52, 52, 52, 1] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 20, 36, 28, 29, 30] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35])
total number of confs: 170
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040845 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040845
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040845/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040845/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040845
Building REAL300000040846
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040846'
/scratch/stefan/7769621/working/building/REAL300000040846 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040846

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040846/0 /scratch/stefan/7769621/working/building/REAL300000040846 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 952)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/952
`/scratch/stefan/7769621/working/3D/952' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=CC(C=NNC2=C3N=CN=C3N=C[N-]2)=C1)

`REAL300000040846.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040846.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040846/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040846 none O=C([O-])CCOC1=CC=CC(C=NNC2=C3N=CN=C3N=C[N-]2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 194, 183, 122, 48, 48, 48, 48, 48, 24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 201, 201, 182, 182, 48, 48, 48, 24, 6, 1, 1, 48] 201
rigid atoms, others: [33, 34, 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, 35])
total number of confs: 589
number of broken/clashed sets: 47
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040846 none O=C([O-])CCOC1=CC=CC(C=NNC2=C3N=CN=C3N=C[N-]2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 36, 40, 26, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 29, 49, 49, 49, 49, 49, 49, 49, 48, 1, 36, 36, 26, 26, 1, 1, 1, 6, 29, 49, 49, 1] 201
rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11, 23, 28, 29, 30] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 285
number of broken/clashed sets: 47
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040846 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040846/1 /scratch/stefan/7769621/working/building/REAL300000040846 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 953)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/953
`/scratch/stefan/7769621/working/3D/953' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=CC(CN=NC2=C3N=CNC3=NC=N2)=C1)

`REAL300000040846.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040846.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040846/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040846 none O=C([O-])CCOC1=CC=CC(CN=NC2=C3N=CNC3=NC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 47, 47, 47, 47, 47, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 201, 201, 201, 201, 47, 47, 47, 12, 13, 1, 1, 1, 47] 201
rigid atoms, others: [33, 34, 35, 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, 36])
total number of confs: 277
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040846 none O=C([O-])CCOC1=CC=CC(CN=NC2=C3N=CNC3=NC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 8, 15, 8, 6, 1, 1, 1, 1, 1, 1, 1, 9, 43, 43, 47, 47, 47, 47, 47, 47, 47, 47, 1, 8, 8, 8, 8, 1, 1, 1, 9, 9, 47, 47, 47, 1] 201
rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 23, 28, 29, 30] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 31, 32, 33, 34, 35])
total number of confs: 120
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040846 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040846
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040846/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040846/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040846
Building REAL300000040847
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040847'
/scratch/stefan/7769621/working/building/REAL300000040847 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040847

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040847/0 /scratch/stefan/7769621/working/building/REAL300000040847 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 954)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/954
`/scratch/stefan/7769621/working/3D/954' -> `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=NNC2=C3N=CN=C3N=C[N-]2)=C1)

`REAL300000040847.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040847.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040847/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040847 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NNC2=C3N=CN=C3N=C[N-]2)=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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.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, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 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, 93, 94, 94, 94, 94, 94, 94, 76, 71, 59, 59, 59, 59, 59, 30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 94, 94, 94, 94, 75, 75, 59, 59, 59, 30, 6, 1, 1, 59] 94
rigid atoms, others: [40, 41, 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, 42])
total number of confs: 163
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040847 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NNC2=C3N=CN=C3N=C[N-]2)=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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.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, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 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: [15, 10, 15, 10, 10, 10, 10, 10, 6, 2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 33, 60, 60, 60, 60, 60, 60, 60, 59, 1, 10, 10, 10, 10, 6, 6, 1, 1, 1, 6, 33, 60, 60, 1] 94
rigid atoms, others: [35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 28, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41])
total number of confs: 164
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040847 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NNC2=C3N=CN=C3N=C[N-]2)=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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.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, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 7, 10, 10, 10, 10, 10, 19, 19, 65, 94, 94, 94, 94, 94, 94, 94, 93, 10, 1, 1, 1, 1, 3, 3, 10, 10, 10, 19, 65, 94, 94, 10] 94
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 232
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040847 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040847/1 /scratch/stefan/7769621/working/building/REAL300000040847 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 955)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/955
`/scratch/stefan/7769621/working/3D/955' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC=C1COC1=CC=CC(CN=NC2=C3N=CNC3=NC=N2)=C1)

`REAL300000040847.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040847.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040847/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040847 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(CN=NC2=C3N=CNC3=NC=N2)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 158, 158, 87, 87, 87, 87, 87, 19, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 87, 201, 201, 201, 201, 158, 158, 87, 87, 87, 18, 19, 1, 1, 1, 87] 201
rigid atoms, others: [40, 41, 42, 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, 43])
total number of confs: 360
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: REAL300000040847 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(CN=NC2=C3N=CNC3=NC=N2)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 6, 9, 6, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 1, 1, 1, 8, 62, 63, 87, 87, 87, 87, 87, 87, 87, 87, 1, 6, 6, 6, 6, 2, 2, 1, 1, 1, 8, 8, 87, 87, 87, 1] 201
rigid atoms, others: [35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 43, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42])
total number of confs: 155
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040847 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(CN=NC2=C3N=CNC3=NC=N2)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 3, 6, 6, 36, 165, 166, 201, 201, 201, 201, 201, 201, 201, 201, 6, 1, 1, 1, 1, 3, 3, 6, 6, 6, 36, 36, 201, 201, 201, 6] 201
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 376
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040847 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040847
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040847/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040847/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040847
Building REAL300000040848
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040848'
/scratch/stefan/7769621/working/building/REAL300000040848 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300000040848

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040848/0 /scratch/stefan/7769621/working/building/REAL300000040848 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 956)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/956
`/scratch/stefan/7769621/working/3D/956' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC2=C3N=CNC3=NC=N2)C=C1[N+](=O)[O-])

`REAL300000040848.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040848.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040848/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040848 none O=C([O-])COC1=CC=C(C=NNC2=C3N=CNC3=NC=N2)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', 'N.pl3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 8, 1, 8, 1, 8, 1, 8, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [31, 31, 31, 31, 19, 19, 21, 21, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 31, 31, 21, 21, 11, 5, 1, 1, 1, 21] 31
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: 62
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040848 none O=C([O-])COC1=CC=C(C=NNC2=C3N=CNC3=NC=N2)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', 'N.pl3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 8, 1, 8, 1, 8, 1, 8, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 7, 7, 17, 20, 21, 21, 21, 20, 21, 21, 21, 1, 1, 1, 2, 2, 5, 5, 1, 1, 7, 17, 21, 21, 21, 1] 31
rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 21, 22, 23, 28, 29] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 30, 31, 32, 33, 34])
total number of confs: 71
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040848 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040848/1 /scratch/stefan/7769621/working/building/REAL300000040848 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 957)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/957
`/scratch/stefan/7769621/working/3D/957' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(CN=NC2=C3N=CNC3=NC=N2)C=C1[N+](=O)[O-])

`REAL300000040848.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040848.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040848/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040848 none O=C([O-])COC1=CC=C(CN=NC2=C3N=CNC3=NC=N2)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 3, 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, 195, 23, 16, 79, 79, 16, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 79, 201, 201, 79, 79, 16, 15, 1, 1, 1, 79] 201
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: 460
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040848 none O=C([O-])COC1=CC=C(CN=NC2=C3N=CNC3=NC=N2)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 3, 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: [25, 17, 25, 7, 1, 1, 1, 1, 1, 1, 9, 55, 55, 79, 79, 79, 79, 79, 79, 79, 79, 1, 1, 1, 2, 2, 17, 17, 1, 1, 9, 9, 79, 79, 79, 1] 201
rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 21, 22, 23, 28, 29] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 30, 31, 32, 33, 34])
total number of confs: 210
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040848 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `2'
/scratch/stefan/7769621/working/building/REAL300000040848/2 /scratch/stefan/7769621/working/building/REAL300000040848 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 2 (index: 958)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/958
`/scratch/stefan/7769621/working/3D/958' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC2=C3NC=NC3=NC=N2)C=C1[N+](=O)[O-])

`REAL300000040848.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300000040848.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040848/2/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`2.mol2' -> `2.mol2.original'
`output.mol2' -> `2.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040848 none O=C([O-])COC1=CC=C(C=NNC2=C3NC=NC3=NC=N2)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', 'N.pl3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 8, 1, 8, 1, 8, 1, 8, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [20, 20, 20, 20, 10, 7, 15, 15, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 20, 20, 15, 15, 4, 2, 1, 1, 1, 15] 20
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: 61
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040848 none O=C([O-])COC1=CC=C(C=NNC2=C3NC=NC3=NC=N2)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', 'N.pl3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 8, 1, 8, 1, 8, 1, 8, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 7, 7, 14, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 2, 2, 5, 5, 1, 1, 7, 14, 15, 15, 15, 1] 20
rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 21, 22, 23, 28, 29] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 30, 31, 32, 33, 34])
total number of confs: 62
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040848 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040848
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
2: /scratch/stefan/7769621/working/building/REAL300000040848/2.*
1: /scratch/stefan/7769621/working/building/REAL300000040848/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040848/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040848
Building REAL300000040849
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040849'
/scratch/stefan/7769621/working/building/REAL300000040849 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040849

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040849/0 /scratch/stefan/7769621/working/building/REAL300000040849 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 959)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/959
`/scratch/stefan/7769621/working/3D/959' -> `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=NNC3=C4N=CN=C4N=C[N-]3)C=C2)=C1)

`REAL300000040849.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040849.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040849/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040849 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=C4N=CN=C4N=C[N-]3)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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 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, 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]
0  hydrogens need rotated
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, 69, 69, 68, 64, 69, 69, 36, 36, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69, 201, 201, 201, 201, 69, 69, 69, 69, 36, 8, 1, 1, 69, 69, 201] 201
rigid atoms, others: [38, 39, 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, 40, 41, 42])
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: REAL300000040849 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=C4N=CN=C4N=C[N-]3)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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 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, 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]
0  hydrogens 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, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 37, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1, 9, 9, 9, 9, 1, 1, 1, 1, 11, 37, 69, 69, 1, 1, 9] 201
rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 14, 40, 41, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 36, 37, 38, 39, 42])
total number of confs: 176
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040849 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=C4N=CN=C4N=C[N-]3)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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 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, 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]
0  hydrogens need rotated
201  conformations 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, 36, 36, 119, 201, 201, 201, 201, 201, 201, 201, 201, 9, 9, 1, 2, 2, 2, 9, 9, 9, 9, 36, 119, 201, 201, 8, 9, 1] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 42, 28] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 432
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040849 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040849/1 /scratch/stefan/7769621/working/building/REAL300000040849 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 960)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/960
`/scratch/stefan/7769621/working/3D/960' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])OC(COC2=CC=C(CN=NC3=C4N=CNC4=NC=N3)C=C2)=C1)

`REAL300000040849.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040849.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040849/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040849 none CC1=C(C(=O)[O-])OC(COC2=CC=C(CN=NC3=C4N=CNC4=NC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 59, 59, 58, 17, 59, 59, 12, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 201, 201, 201, 201, 60, 59, 59, 59, 12, 12, 1, 1, 1, 59, 59, 201] 201
rigid atoms, others: [38, 39, 40, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43])
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: REAL300000040849 none CC1=C(C(=O)[O-])OC(COC2=CC=C(CN=NC3=C4N=CNC4=NC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 6, 11, 11, 6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 53, 53, 59, 59, 59, 59, 59, 59, 59, 59, 1, 1, 6, 6, 6, 6, 1, 1, 1, 1, 8, 8, 59, 59, 59, 1, 1, 6] 201
rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 14, 41, 26, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43])
total number of confs: 116
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040849 none CC1=C(C(=O)[O-])OC(COC2=CC=C(CN=NC3=C4N=CNC4=NC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 35, 189, 189, 201, 201, 201, 201, 201, 201, 201, 201, 6, 6, 1, 2, 2, 2, 6, 6, 6, 6, 35, 35, 201, 201, 201, 5, 6, 1] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 43, 28] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 344
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040849 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040849
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040849/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040849/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040849
Building REAL300000040850
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040850'
/scratch/stefan/7769621/working/building/REAL300000040850 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040850

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040850/0 /scratch/stefan/7769621/working/building/REAL300000040850 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 961)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/961
`/scratch/stefan/7769621/working/3D/961' -> `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=NNC3=C4N=CN=C4N=C[N-]3)=C2)=C1)

`REAL300000040850.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040850.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040850/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040850 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NNC3=C4N=CN=C4N=C[N-]3)=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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.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, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 62, 62, 39, 39, 38, 39, 39, 24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 201, 201, 201, 201, 62, 62, 38, 39, 39, 24, 6, 1, 1, 39, 201] 201
rigid atoms, others: [39, 40, 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, 41, 42])
total number of confs: 295
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: REAL300000040850 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NNC3=C4N=CN=C4N=C[N-]3)=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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.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, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 17, 17, 16, 17, 17, 2, 2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 25, 39, 39, 39, 39, 39, 39, 39, 39, 1, 17, 16, 17, 17, 2, 2, 1, 1, 1, 7, 25, 39, 39, 1, 17] 201
rigid atoms, others: [34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 41, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 42])
total number of confs: 109
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040850 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NNC3=C4N=CN=C4N=C[N-]3)=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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.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, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 9, 9, 17, 17, 17, 17, 17, 50, 50, 157, 201, 201, 201, 201, 201, 201, 201, 201, 17, 1, 1, 1, 1, 9, 9, 17, 17, 17, 50, 157, 201, 201, 17, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 42, 28, 29, 30, 31] set([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])
total number of confs: 500
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040850 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040850/1 /scratch/stefan/7769621/working/building/REAL300000040850 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 962)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/962
`/scratch/stefan/7769621/working/3D/962' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(COC2=CC=CC(CN=NC3=C4N=CNC4=NC=N3)=C2)=C1)

`REAL300000040850.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040850.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040850/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040850 none O=C([O-])C1=CC=CC(COC2=CC=CC(CN=NC3=C4N=CNC4=NC=N3)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.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: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 75, 73, 51, 51, 50, 51, 51, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 201, 201, 201, 201, 75, 75, 50, 51, 51, 20, 20, 1, 1, 1, 51, 201] 201
rigid atoms, others: [39, 40, 41, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43])
total number of confs: 348
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: REAL300000040850 none O=C([O-])C1=CC=CC(COC2=CC=CC(CN=NC3=C4N=CNC4=NC=N3)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.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: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 13, 12, 13, 13, 4, 2, 1, 1, 1, 1, 1, 1, 1, 8, 41, 41, 51, 51, 51, 51, 51, 51, 51, 51, 1, 13, 12, 13, 13, 4, 4, 1, 1, 1, 8, 8, 51, 51, 51, 1, 13] 201
rigid atoms, others: [34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 43])
total number of confs: 106
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040850 none O=C([O-])C1=CC=CC(COC2=CC=CC(CN=NC3=C4N=CNC4=NC=N3)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.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: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 8, 13, 13, 13, 13, 13, 56, 199, 199, 201, 201, 201, 201, 201, 201, 201, 201, 13, 1, 1, 1, 1, 6, 6, 13, 12, 13, 56, 56, 201, 201, 201, 13, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 43, 28, 29, 30, 31] set([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])
total number of confs: 383
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040850 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040850
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040850/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040850/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040850
Building REAL300000040851
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040851'
/scratch/stefan/7769621/working/building/REAL300000040851 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040851

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040851/0 /scratch/stefan/7769621/working/building/REAL300000040851 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 963)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/963
`/scratch/stefan/7769621/working/3D/963' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=CC(C=NNC2=C3N=CN=C3N=C[N-]2)=C1)

`REAL300000040851.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040851.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040851/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040851 none O=C([O-])COC1=CC=CC(C=NNC2=C3N=CN=C3N=C[N-]2)=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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 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, 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, 201, 159, 72, 72, 72, 72, 72, 43, 43, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 72, 200, 200, 72, 72, 72, 43, 6, 1, 1, 72] 201
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 473
number of broken/clashed sets: 32
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040851 none O=C([O-])COC1=CC=CC(C=NNC2=C3N=CN=C3N=C[N-]2)=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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 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, 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: [48, 24, 48, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 27, 73, 73, 73, 73, 73, 73, 73, 72, 1, 24, 24, 1, 1, 1, 6, 27, 73, 73, 1] 201
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 22, 25, 26, 27] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 28, 29, 30, 31])
total number of confs: 273
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040851 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040851/1 /scratch/stefan/7769621/working/building/REAL300000040851 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 964)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/964
`/scratch/stefan/7769621/working/3D/964' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=CC(CN=NC2=C3N=CNC3=NC=N2)=C1)

`REAL300000040851.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040851.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040851/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040851 none O=C([O-])COC1=CC=CC(CN=NC2=C3N=CNC3=NC=N2)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', '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, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 178, 59, 59, 59, 59, 59, 15, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 201, 201, 59, 59, 59, 14, 15, 1, 1, 1, 59] 201
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 409
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040851 none O=C([O-])COC1=CC=CC(CN=NC2=C3N=CNC3=NC=N2)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', '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, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 14, 27, 6, 1, 1, 1, 1, 1, 1, 1, 9, 53, 53, 59, 59, 59, 59, 59, 59, 59, 59, 1, 14, 14, 1, 1, 1, 9, 9, 59, 59, 59, 1] 201
rigid atoms, others: [33, 4, 5, 6, 7, 8, 9, 10, 22, 25, 26, 27] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 28, 29, 30, 31, 32])
total number of confs: 176
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040851 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040851
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040851/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040851/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040851
Building REAL300000040852
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040852'
/scratch/stefan/7769621/working/building/REAL300000040852 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040852

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040852/0 /scratch/stefan/7769621/working/building/REAL300000040852 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 965)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/965
`/scratch/stefan/7769621/working/3D/965' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(COC2=CC=C(C=NNC3=C4N=CN=C4N=C[N-]3)C=C2)OC=C1)

`REAL300000040852.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040852.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040852/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040852 none O=C([O-])C1=C(COC2=CC=C(C=NNC3=C4N=CN=C4N=C[N-]3)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 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, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
135  conformations in input
total number of sets (complete confs): 135
using faster count positions algorithm for large data
unique positions, atoms: [135, 135, 135, 135, 95, 85, 69, 65, 85, 85, 43, 43, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 85, 85, 135, 135, 135, 95, 95, 85, 85, 43, 9, 1, 1, 85, 85, 135, 135] 135
rigid atoms, others: [34, 35, 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, 36, 37, 38, 39])
total number of confs: 314
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: REAL300000040852 none O=C([O-])C1=C(COC2=CC=C(C=NNC3=C4N=CN=C4N=C[N-]3)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 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, 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, 9, 11, 9, 5, 1, 1, 1, 1, 1, 1, 1, 9, 9, 45, 85, 85, 85, 85, 85, 85, 85, 85, 1, 1, 9, 9, 9, 5, 5, 1, 1, 9, 45, 85, 85, 1, 1, 9, 9] 135
rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 23, 24, 37, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 38, 39])
total number of confs: 196
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040852 none O=C([O-])C1=C(COC2=CC=C(C=NNC3=C4N=CN=C4N=C[N-]3)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 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, 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: [3, 1, 3, 1, 1, 1, 5, 9, 9, 9, 9, 9, 35, 35, 108, 135, 135, 135, 135, 135, 135, 135, 135, 9, 9, 1, 1, 1, 5, 5, 9, 9, 35, 108, 135, 135, 9, 9, 1, 1] 135
rigid atoms, others: [1, 3, 4, 5, 38, 39, 25, 26, 27] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 343
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040852 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040852/1 /scratch/stefan/7769621/working/building/REAL300000040852 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 966)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/966
`/scratch/stefan/7769621/working/3D/966' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(COC2=CC=C(CN=NC3=C4N=CNC4=NC=N3)C=C2)OC=C1)

`REAL300000040852.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040852.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040852/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040852 none O=C([O-])C1=C(COC2=CC=C(CN=NC3=C4N=CNC4=NC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', '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, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 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, 200, 140, 132, 131, 48, 132, 132, 42, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 132, 132, 200, 200, 200, 141, 140, 132, 132, 42, 42, 1, 1, 1, 132, 132, 200, 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, 39, 40])
total number of confs: 638
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: REAL300000040852 none O=C([O-])C1=C(COC2=CC=C(CN=NC3=C4N=CNC4=NC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', '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, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 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: [8, 7, 8, 7, 3, 1, 1, 1, 1, 1, 1, 1, 8, 70, 70, 132, 132, 132, 132, 132, 132, 132, 132, 1, 1, 7, 7, 7, 3, 3, 1, 1, 8, 8, 132, 132, 132, 1, 1, 7, 7] 201
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 23, 24, 38, 37, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 39, 40])
total number of confs: 221
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040852 none O=C([O-])C1=C(COC2=CC=C(CN=NC3=C4N=CNC4=NC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', '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, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 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, 5, 7, 7, 7, 7, 7, 40, 151, 151, 201, 201, 201, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 5, 5, 7, 7, 40, 40, 201, 201, 201, 7, 7, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 39, 40, 25, 26, 27] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 384
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040852 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040852
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040852/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040852/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040852
Building REAL300000040853
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040853'
/scratch/stefan/7769621/working/building/REAL300000040853 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040853

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040853/0 /scratch/stefan/7769621/working/building/REAL300000040853 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 967)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/967
`/scratch/stefan/7769621/working/3D/967' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)C(OCC(=O)[O-])=C1)

`REAL300000040853.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040853.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040853/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040853 none COC1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 12, 5, 1, 11, 11, 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, 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
166  conformations in input
total number of sets (complete confs): 166
using faster count positions algorithm for large data
unique positions, atoms: [69, 48, 36, 48, 48, 36, 36, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 121, 162, 166, 166, 48, 69, 69, 69, 48, 48, 36, 7, 1, 1, 162, 162, 48] 166
rigid atoms, others: [32, 33, 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, 34, 35, 36])
total number of confs: 497
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040853 none COC1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 12, 5, 1, 11, 11, 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, 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
166  conformations in input
total number of sets (complete confs): 166
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 4, 4, 17, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 10, 30, 55, 55, 1, 3, 3, 3, 1, 1, 4, 17, 48, 48, 30, 30, 1] 166
rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 24, 36, 28, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35])
total number of confs: 262
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040853 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040853/1 /scratch/stefan/7769621/working/building/REAL300000040853 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 968)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/968
`/scratch/stefan/7769621/working/3D/968' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CN=NC2=C3N=CNC3=NC=N2)C(OCC(=O)[O-])=C1)

`REAL300000040853.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040853.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040853/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040853 none COC1=CC=C(CN=NC2=C3N=CNC3=NC=N2)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.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, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 12, 5, 1, 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, 7, 4, 7, 3, 7, 3, 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: [74, 66, 66, 66, 66, 23, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 66, 152, 201, 201, 201, 66, 74, 74, 74, 66, 66, 22, 23, 1, 1, 1, 201, 201, 66] 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])
total number of confs: 522
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040853 none COC1=CC=C(CN=NC2=C3N=CNC3=NC=N2)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.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, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 12, 5, 1, 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, 7, 4, 7, 3, 7, 3, 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: [2, 1, 1, 1, 1, 1, 1, 6, 37, 38, 66, 66, 66, 66, 66, 66, 66, 66, 1, 1, 8, 28, 48, 48, 1, 3, 3, 3, 1, 1, 6, 6, 66, 66, 66, 28, 28, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 24, 28, 29, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 266
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040853 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040853
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040853/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040853/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040853
Building REAL300000040854
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040854'
/scratch/stefan/7769621/working/building/REAL300000040854 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040854

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040854/0 /scratch/stefan/7769621/working/building/REAL300000040854 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 969)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/969
`/scratch/stefan/7769621/working/3D/969' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)C=C1)

`REAL300000040854.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040854.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040854/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040854 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 200, 201, 148, 201, 201, 56, 56, 71, 71, 33, 33, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 33, 6, 1, 1, 71, 71] 201
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 32, 23, 24, 25, 26, 27, 28, 31])
total number of confs: 537
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040854 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [40, 24, 40, 7, 24, 24, 1, 1, 1, 1, 1, 1, 7, 7, 34, 71, 71, 71, 71, 71, 71, 71, 71, 1, 1, 1, 1, 7, 34, 71, 71, 1, 1] 201
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30])
total number of confs: 263
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040854 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040854/1 /scratch/stefan/7769621/working/building/REAL300000040854 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 970)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/970
`/scratch/stefan/7769621/working/3D/970' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C(F)(F)OC1=CC=C(CN=NC2=C3N=CNC3=NC=N2)C=C1)

`REAL300000040854.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040854.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040854/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040854 none O=C([O-])C(F)(F)OC1=CC=C(CN=NC2=C3N=CNC3=NC=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [197, 196, 197, 124, 196, 196, 10, 10, 45, 45, 10, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 9, 10, 1, 1, 1, 45, 45] 201
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 33, 32, 23, 24, 25, 26, 27, 28])
total number of confs: 620
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040854 none O=C([O-])C(F)(F)OC1=CC=C(CN=NC2=C3N=CNC3=NC=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [25, 19, 25, 7, 19, 19, 1, 1, 1, 1, 1, 1, 8, 44, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 8, 8, 45, 45, 45, 1, 1] 201
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 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/7769621/working/building/REAL300000040854 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040854
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040854/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040854/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040854
Building REAL300000040855
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040855'
/scratch/stefan/7769621/working/building/REAL300000040855 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040855

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040855/0 /scratch/stefan/7769621/working/building/REAL300000040855 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 971)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/971
`/scratch/stefan/7769621/working/3D/971' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=C2N=CN=C2NC=N1)

`REAL300000040855.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040855.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040855/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040855 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=C2N=CN=C2NC=N1 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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 32, 23, 23, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 23, 8, 1, 1, 1] 32
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27])
total number of confs: 53
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040855 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=C2N=CN=C2NC=N1 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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 8, 8, 27, 32, 32, 32, 32, 32, 32, 32, 32, 2, 2, 2, 1, 8, 27, 32, 32, 32] 32
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 25] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30])
total number of confs: 83
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040855 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040855
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040855/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040855
Building REAL300000040856
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040856'
/scratch/stefan/7769621/working/building/REAL300000040856 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040856

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040856/0 /scratch/stefan/7769621/working/building/REAL300000040856 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 972)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/972
`/scratch/stefan/7769621/working/3D/972' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)C=C1Br)

`REAL300000040856.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040856.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040856/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040856 none O=C([O-])COC1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'Br', '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, 8, 1, 8, 1, 8, 1, 8, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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]
0  hydrogens need rotated
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, 81, 64, 81, 81, 34, 34, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 201, 201, 81, 81, 34, 6, 1, 1, 81] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 570
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040856 none O=C([O-])COC1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'Br', '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, 8, 1, 8, 1, 8, 1, 8, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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]
0  hydrogens 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, 28, 52, 7, 1, 1, 1, 1, 1, 1, 6, 6, 38, 81, 81, 81, 81, 81, 81, 81, 81, 1, 1, 1, 28, 28, 1, 1, 6, 38, 81, 81, 1] 201
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 21, 22, 23, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 28, 29, 30, 31])
total number of confs: 314
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040856 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040856
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040856/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040856
Building REAL300000040857
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040857'
/scratch/stefan/7769621/working/building/REAL300000040857 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040857

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040857/0 /scratch/stefan/7769621/working/building/REAL300000040857 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 973)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/973
`/scratch/stefan/7769621/working/3D/973' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=C3N=CN=C3NC=N2)C=C1)

`REAL300000040857.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040857.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040857/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040857 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=C3N=CN=C3NC=N2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', '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, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 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, 55, 55, 55, 55, 55, 55, 55, 55, 35, 35, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55, 35, 11, 1, 1, 1, 55, 55] 55
rigid atoms, others: [32, 33, 34, 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, 35, 36])
total number of confs: 87
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040857 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=C3N=CN=C3NC=N2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', '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, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 10, 10, 29, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 3, 3, 3, 1, 10, 29, 55, 55, 55, 1, 1] 55
rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 35, 24, 25, 29, 36] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34])
total number of confs: 112
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040857 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040857
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040857/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040857
Building REAL300000040858
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040858'
/scratch/stefan/7769621/working/building/REAL300000040858 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040858

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040858/0 /scratch/stefan/7769621/working/building/REAL300000040858 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 974)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/974
`/scratch/stefan/7769621/working/3D/974' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC1=C2N=CN=C2NC=N1)C1=CC=C(C(=O)[O-])C=C1)

`REAL300000040858.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040858.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040858/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040858 none CCC(=NNC1=C2N=CN=C2NC=N1)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 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, 7, 7, 2, 2, 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: [19, 6, 1, 6, 6, 35, 74, 74, 74, 74, 74, 74, 74, 74, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 35, 74, 74, 74, 1, 1, 1, 1] 79
rigid atoms, others: [32, 33, 2, 35, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 204
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040858 none CCC(=NNC1=C2N=CN=C2NC=N1)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 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, 7, 7, 2, 2, 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: [64, 43, 43, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 74, 74, 46, 46, 74, 74, 74, 74, 64, 64, 64, 64, 64, 10, 1, 1, 1, 74, 74, 74, 74] 79
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35])
total number of confs: 399
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040858 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040858
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040858/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040858
Building REAL300000040859
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040859'
/scratch/stefan/7769621/working/building/REAL300000040859 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040859

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040859/0 /scratch/stefan/7769621/working/building/REAL300000040859 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 975)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/975
`/scratch/stefan/7769621/working/3D/975' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2N=CN=C2NC=N1)C1=CC(C(=O)[O-])=CC=C1O)

`REAL300000040859.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040859.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040859/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040859 none CC(=NNC1=C2N=CN=C2NC=N1)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [9, 1, 9, 9, 35, 61, 61, 61, 61, 61, 61, 61, 61, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 9, 9, 35, 61, 61, 61, 1, 1, 1, 2] 122
rigid atoms, others: [32, 1, 13, 14, 15, 16, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 133
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040859 none CC(=NNC1=C2N=CN=C2NC=N1)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [32, 32, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 61, 61, 61, 61, 61, 61, 61, 61, 61, 33, 33, 33, 10, 1, 1, 1, 61, 61, 61, 122] 122
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: 229
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040859 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040859
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040859/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040859
Building REAL300000040860
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040860'
/scratch/stefan/7769621/working/building/REAL300000040860 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040860

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040860/0 /scratch/stefan/7769621/working/building/REAL300000040860 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 976)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/976
`/scratch/stefan/7769621/working/3D/976' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC1=C2N=CN=C2NC=N1)C1=CC(C(=O)[O-])=CC=C1F)

`REAL300000040860.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040860.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040860/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040860 none CCC(=NNC1=C2N=CN=C2NC=N1)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 6, 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, 7, 2, 2, 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: [32, 12, 1, 12, 12, 62, 138, 138, 138, 138, 138, 138, 138, 138, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 62, 138, 138, 138, 1, 1, 1] 157
rigid atoms, others: [33, 2, 35, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 364
number of broken/clashed sets: 31
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040860 none CCC(=NNC1=C2N=CN=C2NC=N1)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 6, 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, 7, 2, 2, 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: [86, 42, 42, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 138, 138, 138, 138, 138, 138, 138, 138, 138, 86, 86, 86, 86, 86, 10, 1, 1, 1, 138, 138, 138] 157
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])
total number of confs: 413
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040860 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040860
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040860/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040860
Building REAL300000040861
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040861'
/scratch/stefan/7769621/working/building/REAL300000040861 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040861

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040861/0 /scratch/stefan/7769621/working/building/REAL300000040861 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 977)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/977
`/scratch/stefan/7769621/working/3D/977' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(C=NNC3=C4N=CN=C4N=C[N-]3)=NNC2=C1)

`REAL300000040861.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040861.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040861/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040861 none O=C([O-])C1=CC=C2C(C=NNC3=C4N=CN=C4N=C[N-]3)=NNC2=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', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [81, 81, 81, 81, 81, 81, 81, 48, 48, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 81, 48, 12, 1, 1, 81, 81] 81
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 130
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040861 none O=C([O-])C1=CC=C2C(C=NNC3=C4N=CN=C4N=C[N-]3)=NNC2=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', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 58, 81, 81, 81, 81, 81, 81, 81, 81, 1, 1, 1, 1, 1, 1, 11, 58, 81, 81, 1, 1] 81
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 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/7769621/working/building/REAL300000040861 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040861
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040861/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040861
Building REAL300000040862
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040862'
/scratch/stefan/7769621/working/building/REAL300000040862 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040862

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040862/0 /scratch/stefan/7769621/working/building/REAL300000040862 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 978)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/978
`/scratch/stefan/7769621/working/3D/978' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2N=CN=C2NC=N1)C1=CC=C(C(=O)[O-])C(F)=C1)

`REAL300000040862.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040862.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040862/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040862 none CC(=NNC1=C2N=CN=C2NC=N1)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 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, 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, 56, 115, 115, 115, 115, 115, 115, 115, 115, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 11, 11, 11, 56, 115, 115, 115, 1, 1, 1] 115
rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 234
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040862 none CC(=NNC1=C2N=CN=C2NC=N1)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 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, 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: [48, 48, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 115, 115, 115, 115, 115, 115, 115, 115, 115, 49, 49, 49, 10, 1, 1, 1, 115, 115, 115] 115
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: 177
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040862 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040862
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040862/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040862
Building REAL300000040863
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040863'
/scratch/stefan/7769621/working/building/REAL300000040863 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040863

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040863/0 /scratch/stefan/7769621/working/building/REAL300000040863 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 979)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/979
`/scratch/stefan/7769621/working/3D/979' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=C3N=CNC3=NC=N2)=C([N+](=O)[O-])C=C1OCC(=O)[O-])

`REAL300000040863.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040863.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040863/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040863 none COC1=CC(C=NNC2=C3N=CNC3=NC=N2)=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.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 3, 3, 7, 7, 3, 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: [117, 74, 74, 74, 30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 74, 74, 74, 172, 201, 201, 201, 117, 117, 117, 74, 30, 6, 1, 1, 1, 74, 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])
total number of confs: 489
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040863 none COC1=CC(C=NNC2=C3N=CNC3=NC=N2)=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.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 3, 3, 7, 7, 3, 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: [3, 1, 1, 1, 1, 1, 7, 7, 37, 74, 74, 74, 74, 74, 74, 74, 74, 1, 1, 2, 2, 1, 1, 1, 9, 17, 26, 26, 4, 4, 4, 1, 7, 37, 74, 74, 74, 1, 17, 17] 201
rigid atoms, others: [1, 2, 3, 4, 5, 17, 18, 21, 22, 23, 37, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 238
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040863 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040863/1 /scratch/stefan/7769621/working/building/REAL300000040863 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 980)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/980
`/scratch/stefan/7769621/working/3D/980' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=C3NC=NC3=NC=N2)=C([N+](=O)[O-])C=C1OCC(=O)[O-])

`REAL300000040863.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040863.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040863/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040863 none COC1=CC(C=NNC2=C3NC=NC3=NC=N2)=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.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 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: [70, 35, 35, 35, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 95, 124, 124, 124, 70, 70, 70, 35, 10, 4, 1, 1, 1, 35, 124, 124] 124
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])
total number of confs: 369
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040863 none COC1=CC(C=NNC2=C3NC=NC3=NC=N2)=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.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
124  conformations in input
total number of sets (complete confs): 124
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 17, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 2, 2, 1, 1, 1, 7, 15, 22, 22, 4, 4, 4, 1, 7, 17, 35, 35, 35, 1, 15, 15] 124
rigid atoms, others: [1, 2, 3, 4, 5, 17, 18, 21, 22, 23, 37, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 167
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040863 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040863
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040863/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040863/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040863
Building REAL300000040864
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040864'
/scratch/stefan/7769621/working/building/REAL300000040864 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040864

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040864/0 /scratch/stefan/7769621/working/building/REAL300000040864 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 981)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/981
`/scratch/stefan/7769621/working/3D/981' -> `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=NNC1=C2N=CN=C2N=C[N-]1)

`REAL300000040864.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040864.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040864/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040864 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNC1=C2N=CN=C2N=C[N-]1 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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', '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, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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]
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: [23, 23, 23, 24, 24, 24, 23, 23, 23, 23, 23, 23, 23, 23, 23, 19, 19, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 24, 24, 23, 23, 23, 19, 10, 1, 1] 24
rigid atoms, others: [38, 39, 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])
total number of confs: 50
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040864 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNC1=C2N=CN=C2N=C[N-]1 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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', '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, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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]
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: [3, 1, 3, 5, 9, 9, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 3, 3, 8, 23, 23, 23, 23, 23, 23, 23, 23, 3, 3, 3, 5, 5, 1, 1, 1, 3, 8, 23, 23] 24
rigid atoms, others: [1, 34, 35, 33, 6, 7, 8, 9, 10, 14, 15, 16] set([0, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39])
total number of confs: 79
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040864 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040864
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040864/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040864
Building REAL300000040865
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040865'
/scratch/stefan/7769621/working/building/REAL300000040865 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040865

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040865/0 /scratch/stefan/7769621/working/building/REAL300000040865 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 982)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/982
`/scratch/stefan/7769621/working/3D/982' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2N=CN=C2NC=N1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1)

`REAL300000040865.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040865.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040865/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040865 none CC(=NNC1=C2N=CN=C2NC=N1)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 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, 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: [70, 19, 70, 70, 162, 201, 201, 201, 201, 201, 201, 201, 201, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 19, 19, 70, 70, 70, 162, 201, 201, 201, 19, 19, 1, 1, 1, 1, 19, 19] 201
rigid atoms, others: [38, 39, 40, 41, 17, 18, 19, 20, 21, 22, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43])
total number of confs: 512
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: REAL300000040865 none CC(=NNC1=C2N=CN=C2NC=N1)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 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, 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: [6, 1, 6, 6, 30, 70, 70, 70, 70, 70, 70, 70, 70, 1, 1, 1, 1, 1, 9, 19, 19, 11, 11, 19, 19, 19, 19, 1, 1, 7, 7, 7, 29, 70, 70, 70, 1, 1, 19, 19, 19, 19, 1, 1] 201
rigid atoms, others: [1, 36, 37, 42, 43, 13, 14, 15, 16, 17, 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])
total number of confs: 199
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040865 none CC(=NNC1=C2N=CN=C2NC=N1)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 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, 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, 32, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 70, 70, 43, 70, 184, 201, 201, 184, 184, 201, 201, 201, 201, 70, 70, 33, 33, 33, 6, 1, 1, 1, 70, 70, 201, 201, 201, 201, 70, 70] 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])
total number of confs: 513
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040865 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040865
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040865/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040865
Building REAL300000040866
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040866'
/scratch/stefan/7769621/working/building/REAL300000040866 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040866

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040866/0 /scratch/stefan/7769621/working/building/REAL300000040866 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 983)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/983
`/scratch/stefan/7769621/working/3D/983' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=C3N=CN=C3N=C[N-]2)=CC=C1OCCC(=O)[O-])

`REAL300000040866.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040866.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040866/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040866 none COC1=CC(C=NNC2=C3N=CN=C3N=C[N-]2)=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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [105, 61, 61, 61, 22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 61, 61, 60, 60, 162, 195, 195, 201, 194, 105, 105, 105, 61, 22, 6, 1, 1, 61, 61, 195, 195, 195, 195] 201
rigid atoms, others: [32, 33, 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, 34, 35, 36, 37, 38, 39])
total number of confs: 518
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040866 none COC1=CC(C=NNC2=C3N=CN=C3N=C[N-]2)=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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 37, 61, 61, 61, 61, 61, 61, 61, 61, 1, 1, 1, 1, 9, 23, 23, 39, 37, 3, 3, 3, 1, 7, 37, 61, 61, 1, 1, 23, 23, 23, 23] 201
rigid atoms, others: [1, 2, 3, 4, 5, 35, 34, 17, 18, 19, 20, 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, 36, 37, 38, 39])
total number of confs: 258
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040866 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040866
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040866/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040866
Building REAL300000040867
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040867'
/scratch/stefan/7769621/working/building/REAL300000040867 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040867

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040867/0 /scratch/stefan/7769621/working/building/REAL300000040867 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 984)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/984
`/scratch/stefan/7769621/working/3D/984' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)C(Cl)=C1)

`REAL300000040867.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040867.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040867/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040867 none O=C([O-])C1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 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]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [46, 46, 46, 46, 46, 46, 36, 36, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 36, 12, 1, 1, 46] 46
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 28])
total number of confs: 77
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040867 none O=C([O-])C1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 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]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 31, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 9, 31, 46, 46, 1] 46
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27])
total number of confs: 99
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040867 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040867
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040867/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040867
Building REAL300000040868
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040868'
/scratch/stefan/7769621/working/building/REAL300000040868 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040868

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040868/0 /scratch/stefan/7769621/working/building/REAL300000040868 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 985)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/985
`/scratch/stefan/7769621/working/3D/985' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2N=CN=C2NC=N1)C1=CC(C(=O)[O-])=C(C)N=C1C)

`REAL300000040868.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040868.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040868/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040868 none CC(=NNC1=C2N=CN=C2NC=N1)C1=CC(C(=O)[O-])=C(C)N=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.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, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 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]
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, 47, 82, 82, 82, 82, 82, 82, 82, 82, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 9, 9, 9, 47, 82, 82, 82, 1, 2, 2, 2, 2, 2, 2] 82
rigid atoms, others: [1, 13, 14, 15, 16, 19, 20, 21, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37])
total number of confs: 180
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040868 none CC(=NNC1=C2N=CN=C2NC=N1)C1=CC(C(=O)[O-])=C(C)N=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.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, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 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]
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: [44, 44, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 45, 45, 45, 10, 1, 1, 1, 82, 82, 82, 82, 82, 82, 82] 82
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: 130
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040868 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040868
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040868/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040868
Building REAL300000040869
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040869'
/scratch/stefan/7769621/working/building/REAL300000040869 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040869

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040869/0 /scratch/stefan/7769621/working/building/REAL300000040869 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 986)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/986
`/scratch/stefan/7769621/working/3D/986' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2N=CN=C2NC=N1)C1=CC(C(=O)[O-])=CC=C1C)

`REAL300000040869.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040869.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040869/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040869 none CC(=NNC1=C2N=CN=C2NC=N1)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 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, 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: [9, 1, 9, 9, 32, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 9, 9, 32, 49, 49, 49, 1, 1, 1, 2, 2, 2] 49
rigid atoms, others: [32, 1, 13, 14, 15, 16, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35])
total number of confs: 118
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040869 none CC(=NNC1=C2N=CN=C2NC=N1)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 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, 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: [31, 31, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 49, 49, 49, 49, 49, 49, 49, 49, 49, 32, 32, 32, 10, 1, 1, 1, 49, 49, 49, 49, 49, 49] 49
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: 85
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040869 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040869
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040869/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040869
Building REAL300000040870
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040870'
/scratch/stefan/7769621/working/building/REAL300000040870 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040870

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040870/0 /scratch/stefan/7769621/working/building/REAL300000040870 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 987)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/987
`/scratch/stefan/7769621/working/3D/987' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)C=C1)C(=O)[O-])

`REAL300000040870.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040870.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040870/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040870 none CC(OC1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 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]
0  hydrogens need 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, 84, 83, 114, 114, 47, 47, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 114, 114, 201, 201, 201, 201, 201, 201, 201, 114, 114, 47, 8, 1, 1, 114, 114] 201
rigid atoms, others: [32, 33, 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, 34, 35])
total number of confs: 569
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040870 none CC(OC1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 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]
0  hydrogens 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, 11, 11, 46, 115, 115, 115, 115, 115, 115, 115, 115, 1, 1, 14, 22, 22, 14, 14, 14, 14, 1, 1, 11, 46, 115, 115, 1, 1] 201
rigid atoms, others: [35, 2, 3, 4, 5, 6, 7, 34, 19, 20, 28, 29] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33])
total number of confs: 278
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040870 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040870/1 /scratch/stefan/7769621/working/building/REAL300000040870 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 988)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/988
`/scratch/stefan/7769621/working/3D/988' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=C(CN=NC2=C3N=CNC3=NC=N2)C=C1)C(=O)[O-])

`REAL300000040870.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040870.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040870/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040870 none CC(OC1=CC=C(CN=NC2=C3N=CNC3=NC=N2)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.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, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 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, 158, 68, 16, 85, 85, 16, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 85, 85, 201, 201, 201, 201, 201, 201, 201, 85, 85, 16, 16, 1, 1, 1, 85, 85] 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])
total number of confs: 684
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040870 none CC(OC1=CC=C(CN=NC2=C3N=CNC3=NC=N2)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.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, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 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: [12, 4, 1, 1, 1, 1, 1, 1, 8, 59, 59, 85, 85, 85, 85, 85, 85, 85, 85, 1, 1, 12, 18, 18, 12, 12, 12, 12, 1, 1, 8, 8, 85, 85, 85, 1, 1] 201
rigid atoms, others: [35, 2, 3, 4, 5, 6, 7, 19, 20, 36, 28, 29] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34])
total number of confs: 196
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040870 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040870
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040870/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040870/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040870
Building REAL300000040871
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040871'
/scratch/stefan/7769621/working/building/REAL300000040871 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040871

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040871/0 /scratch/stefan/7769621/working/building/REAL300000040871 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 989)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/989
`/scratch/stefan/7769621/working/3D/989' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1CCC(=NNC2=C3N=CN=C3NC=N2)C2=CC=CC=C21)

`REAL300000040871.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040871.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040871/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040871 none O=C([O-])C1CCC(=NNC2=C3N=CN=C3NC=N2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.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']
dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 17, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 17, 17, 17, 17] 17
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: 31
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040871 none O=C([O-])C1CCC(=NNC2=C3N=CN=C3NC=N2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.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']
dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 8, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 17, 17, 17, 1, 1, 1, 1] 17
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36] set([0, 32, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31])
total number of confs: 34
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040871 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040871
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040871/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040871
Building REAL300000040872
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040872'
/scratch/stefan/7769621/working/building/REAL300000040872 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040872

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040872/0 /scratch/stefan/7769621/working/building/REAL300000040872 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 990)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/990
`/scratch/stefan/7769621/working/3D/990' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CN1C=C(C=NNC2=C3N=CN=C3NC=N2)C2=CC=CC=C21)

`REAL300000040872.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040872.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040872/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040872 none O=C([O-])CN1C=C(C=NNC2=C3N=CN=C3NC=N2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.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']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 75, 75, 75, 30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 75, 119, 119, 75, 30, 6, 1, 1, 1, 75, 75, 75, 75] 119
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, 35, 36])
total number of confs: 323
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040872 none O=C([O-])CN1C=C(C=NNC2=C3N=CN=C3NC=N2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.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']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 8, 16, 1, 1, 1, 1, 1, 8, 8, 45, 75, 75, 75, 75, 75, 75, 75, 75, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 44, 75, 75, 75, 1, 1, 1, 1] 119
rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 36, 27, 35] set([0, 1, 2, 32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 28, 29, 30, 31])
total number of confs: 203
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040872 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040872
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040872/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040872
Building REAL300000040873
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040873'
/scratch/stefan/7769621/working/building/REAL300000040873 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040873

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040873/0 /scratch/stefan/7769621/working/building/REAL300000040873 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 991)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/991
`/scratch/stefan/7769621/working/3D/991' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2N=CN=C2NC=N1)C1=CC=CC(OCCCC(=O)[O-])=C1)

`REAL300000040873.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040873.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040873/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040873 none CC(=NNC1=C2N=CN=C2NC=N1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 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, 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, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 29, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 6, 21, 35, 58, 80, 80, 1, 11, 11, 11, 29, 30, 30, 30, 1, 1, 1, 21, 21, 35, 35, 58, 58, 1] 201
rigid atoms, others: [1, 34, 35, 33, 42, 13, 14, 15, 16, 17, 18, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41])
total number of confs: 409
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040873 none CC(=NNC1=C2N=CN=C2NC=N1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 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, 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, 7, 7, 7, 7]
0  hydrogens 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, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 30, 30, 30, 30, 30, 86, 127, 153, 201, 201, 201, 30, 7, 7, 7, 3, 1, 1, 1, 30, 30, 30, 127, 127, 153, 153, 201, 201, 30] 201
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])
total number of confs: 707
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040873 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040873
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040873/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040873
Building REAL300000040874
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040874'
/scratch/stefan/7769621/working/building/REAL300000040874 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040874

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040874/0 /scratch/stefan/7769621/working/building/REAL300000040874 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 992)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/992
`/scratch/stefan/7769621/working/3D/992' -> `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=NC1=C2N=CNC2=NC=N1)

`REAL300000040874.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040874.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040874/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040874 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=C2N=CNC2=NC=N1 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.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 7, 23, 48, 54, 54, 54, 54, 54, 169, 201, 201, 201, 201, 54, 54, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 53, 53, 54, 53, 54, 54, 201, 201, 201, 201, 54, 54, 1, 1, 1] 201
rigid atoms, others: [43, 44, 45, 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, 41, 42])
total number of confs: 563
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040874 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=C2N=CNC2=NC=N1 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.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 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: [9, 3, 2, 1, 1, 1, 1, 1, 1, 11, 25, 25, 31, 31, 1, 1, 9, 39, 39, 54, 54, 54, 54, 54, 54, 54, 54, 9, 9, 9, 9, 3, 3, 2, 2, 1, 1, 25, 25, 25, 25, 1, 1, 54, 54, 54] 201
rigid atoms, others: [35, 4, 5, 6, 7, 8, 41, 42, 14, 15, 3, 36] 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, 33, 34, 37, 38, 39, 40, 43, 44, 45])
total number of confs: 188
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040874 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040874
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040874/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040874
Building REAL300000040875
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040875'
/scratch/stefan/7769621/working/building/REAL300000040875 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040875

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040875/0 /scratch/stefan/7769621/working/building/REAL300000040875 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 993)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/993
`/scratch/stefan/7769621/working/3D/993' -> `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=NC1=C2N=CNC2=NC=N1)

`REAL300000040875.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040875.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040875/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040875 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=C2N=CNC2=NC=N1 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.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.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: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 7, 26, 55, 60, 60, 60, 60, 60, 148, 201, 201, 201, 60, 60, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 58, 58, 60, 59, 60, 60, 201, 201, 60, 60, 1, 1, 1] 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])
total number of confs: 654
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040875 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=C2N=CNC2=NC=N1 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.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.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: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 3, 2, 1, 1, 1, 1, 1, 1, 6, 19, 32, 32, 1, 1, 9, 41, 41, 60, 60, 60, 60, 60, 60, 60, 60, 9, 9, 9, 9, 3, 3, 2, 2, 1, 1, 20, 20, 1, 1, 60, 60, 60] 201
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 39, 13, 14, 35, 38] 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, 32, 33, 36, 37, 40, 41, 42])
total number of confs: 208
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040875 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040875
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040875/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040875
Building REAL300000040876
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040876'
/scratch/stefan/7769621/working/building/REAL300000040876 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040876

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040876/0 /scratch/stefan/7769621/working/building/REAL300000040876 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 994)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/994
`/scratch/stefan/7769621/working/3D/994' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2N=CN=C2NC=N1)C1=CC=CC(OC(C)C(=O)[O-])=C1)

`REAL300000040876.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040876.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040876/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040876 none CC(=NNC1=C2N=CN=C2NC=N1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.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', '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, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 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, 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: [10, 1, 10, 10, 37, 56, 56, 56, 56, 56, 56, 56, 56, 1, 1, 1, 1, 1, 1, 11, 30, 30, 44, 44, 1, 10, 10, 10, 37, 56, 56, 56, 1, 1, 1, 30, 30, 30, 30, 1] 201
rigid atoms, others: [32, 1, 34, 33, 39, 13, 14, 15, 16, 17, 18, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38])
total number of confs: 267
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040876 none CC(=NNC1=C2N=CN=C2NC=N1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.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', '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, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 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, 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: [17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 56, 56, 56, 56, 56, 167, 201, 201, 201, 201, 56, 18, 18, 18, 4, 1, 1, 1, 56, 56, 56, 201, 201, 201, 201, 56] 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])
total number of confs: 436
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040876 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040876
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040876/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040876
Building REAL300000040877
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040877'
/scratch/stefan/7769621/working/building/REAL300000040877 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040877

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040877/0 /scratch/stefan/7769621/working/building/REAL300000040877 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 995)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/995
`/scratch/stefan/7769621/working/3D/995' -> `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=NC1=C2N=CNC2=NC=N1)

`REAL300000040877.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040877.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040877/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040877 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=C2N=CNC2=NC=N1 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.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 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: [31, 7, 31, 54, 58, 58, 58, 58, 58, 190, 201, 201, 201, 201, 58, 58, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 56, 56, 58, 58, 58, 58, 201, 201, 201, 201, 58, 58, 1, 1, 1] 201
rigid atoms, others: [43, 44, 45, 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, 41, 42])
total number of confs: 474
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040877 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=C2N=CNC2=NC=N1 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.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 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: [8, 3, 2, 1, 1, 1, 1, 1, 1, 6, 13, 14, 20, 20, 1, 1, 8, 36, 36, 58, 58, 58, 58, 58, 58, 58, 58, 8, 8, 8, 8, 3, 3, 2, 2, 1, 1, 13, 14, 13, 13, 1, 1, 58, 58, 58] 201
rigid atoms, others: [35, 4, 5, 6, 7, 8, 41, 42, 14, 15, 3, 36] 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, 33, 34, 37, 38, 39, 40, 43, 44, 45])
total number of confs: 167
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040877 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040877
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040877/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040877
Building REAL300000040878
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040878'
/scratch/stefan/7769621/working/building/REAL300000040878 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040878

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040878/0 /scratch/stefan/7769621/working/building/REAL300000040878 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 996)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/996
`/scratch/stefan/7769621/working/3D/996' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC1=C2N=CN=C2NC=N1)C1=CC=C(OCCCCC(=O)[O-])C=C1)

`REAL300000040878.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040878.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040878/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040878 none CCC(=NNC1=C2N=CN=C2NC=N1)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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 4, 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]
0  hydrogens 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, 1, 7, 7, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 6, 10, 24, 30, 51, 58, 59, 1, 1, 10, 10, 10, 10, 10, 23, 23, 23, 23, 1, 1, 10, 10, 24, 24, 31, 31, 50, 50, 1, 1] 201
rigid atoms, others: [48, 2, 37, 38, 47, 14, 15, 16, 17, 18, 26, 27] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 334
number of broken/clashed sets: 37
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040878 none CCC(=NNC1=C2N=CN=C2NC=N1)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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 4, 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]
0  hydrogens 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, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 23, 23, 7, 7, 50, 86, 136, 150, 195, 190, 199, 23, 23, 11, 11, 11, 11, 11, 2, 1, 1, 1, 23, 23, 86, 86, 139, 139, 150, 150, 195, 195, 23, 23] 201
rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 36] set([0, 1, 2, 3, 14, 15, 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, 45, 46, 47, 48])
total number of confs: 919
number of broken/clashed sets: 37
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040878 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040878
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040878/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040878
Building REAL300000040879
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040879'
/scratch/stefan/7769621/working/building/REAL300000040879 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040879

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040879/0 /scratch/stefan/7769621/working/building/REAL300000040879 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 997)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/997
`/scratch/stefan/7769621/working/3D/997' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2N=CN=C2NC=N1)C1=CSC(C(=O)[O-])=C1)

`REAL300000040879.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040879.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040879/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040879 none CC(=NNC1=C2N=CN=C2NC=N1)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [11, 1, 11, 11, 46, 60, 60, 60, 60, 60, 60, 60, 60, 1, 1, 1, 1, 1, 2, 2, 1, 12, 12, 12, 46, 60, 60, 60, 1, 1] 60
rigid atoms, others: [1, 13, 14, 15, 16, 17, 20, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 147
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040879 none CC(=NNC1=C2N=CN=C2NC=N1)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [30, 30, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 60, 60, 60, 60, 60, 60, 60, 31, 31, 31, 8, 1, 1, 1, 60, 60] 60
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])
total number of confs: 99
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040879 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040879
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040879/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040879
Building REAL300000040880
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040880'
/scratch/stefan/7769621/working/building/REAL300000040880 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040880

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040880/0 /scratch/stefan/7769621/working/building/REAL300000040880 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 998)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/998
`/scratch/stefan/7769621/working/3D/998' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=C3N=CNC3=NC=N2)C1)

`REAL300000040880.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040880.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040880/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040880 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=C3N=CNC3=NC=N2)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.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', '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, 5, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [44, 34, 44, 34, 34, 44, 44, 38, 44, 44, 34, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 44, 44, 44, 44, 44, 34, 34, 34, 1, 1, 1, 34, 34] 44
rigid atoms, others: [32, 33, 34, 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, 35, 36])
total number of confs: 164
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: REAL300000040880 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=C3N=CNC3=NC=N2)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.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', '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, 5, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [9, 6, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 28, 28, 44, 44, 44, 44, 44, 44, 44, 44, 6, 1, 1, 1, 1, 1, 6, 6, 6, 44, 44, 44, 6, 6] 44
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 27, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 77
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040880 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=C3N=CNC3=NC=N2)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.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', '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, 5, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 6, 6, 2, 6, 6, 1, 1, 1, 13, 13, 34, 34, 34, 34, 34, 34, 34, 34, 1, 6, 6, 3, 6, 6, 1, 1, 1, 34, 34, 34, 1, 1] 44
rigid atoms, others: [1, 3, 4, 10, 11, 12, 35, 23, 36, 29, 30, 31] set([0, 2, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 32, 33, 34])
total number of confs: 64
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040880 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040880
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040880/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040880
Building REAL300000040881
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040881'
/scratch/stefan/7769621/working/building/REAL300000040881 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040881

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040881/0 /scratch/stefan/7769621/working/building/REAL300000040881 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 999)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/999
`/scratch/stefan/7769621/working/3D/999' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=C2N=CNC2=NC=N1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C)

`REAL300000040881.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040881.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040881/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040881 none CC(N=NC1=C2N=CNC2=NC=N1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 5, 7, 5, 5, 7, 5, 1, 11, 11, 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, 7, 7, 7, 7, 7, 4, 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, 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: [4, 1, 4, 21, 21, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 7, 13, 13, 1, 1, 1, 4, 4, 4, 4, 49, 49, 49, 1, 1, 7, 7, 2, 2, 2, 2, 2, 2] 68
rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 127
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040881 none CC(N=NC1=C2N=CNC2=NC=N1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 5, 7, 5, 5, 7, 5, 1, 11, 11, 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, 7, 7, 7, 7, 7, 4, 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, 7]
0  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [35, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 49, 49, 49, 49, 49, 68, 68, 68, 49, 49, 49, 35, 35, 35, 35, 1, 1, 1, 49, 49, 68, 68, 49, 49, 49, 49, 49, 49] 68
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])
total number of confs: 268
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040881 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040881
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040881/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040881
Building REAL300000040882
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040882'
/scratch/stefan/7769621/working/building/REAL300000040882 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040882

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040882/0 /scratch/stefan/7769621/working/building/REAL300000040882 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1000)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1000
`/scratch/stefan/7769621/working/3D/1000' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCCCCCC(=O)[O-])N=NC1=C2N=CNC2=NC=N1)

`REAL300000040882.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040882.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040882/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040882 none CC(CCCCCCC(=O)[O-])N=NC1=C2N=CNC2=NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 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: [39, 8, 39, 73, 84, 94, 121, 131, 200, 201, 201, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 80, 80, 84, 81, 102, 102, 122, 118, 138, 138, 197, 195, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 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])
total number of confs: 984
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040882 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040882
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040882/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040882
Building REAL300000040883
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040883'
/scratch/stefan/7769621/working/building/REAL300000040883 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040883

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040883/0 /scratch/stefan/7769621/working/building/REAL300000040883 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1001)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1001
`/scratch/stefan/7769621/working/3D/1001' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2N=CN=C2NC=N1)C1=CC(C(=O)[O-])=CS1)

`REAL300000040883.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040883.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040883/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040883 none CC(=NNC1=C2N=CN=C2NC=N1)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [13, 1, 12, 12, 50, 76, 76, 76, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 49, 76, 76, 76, 1, 1] 76
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 167
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040883 none CC(=NNC1=C2N=CN=C2NC=N1)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [38, 38, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 75, 75, 76, 76, 75, 75, 76, 39, 39, 39, 8, 1, 1, 1, 76, 76] 76
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])
total number of confs: 125
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040883 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040883
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040883/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040883
Building REAL300000040884
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040884'
/scratch/stefan/7769621/working/building/REAL300000040884 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040884

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040884/0 /scratch/stefan/7769621/working/building/REAL300000040884 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1002)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1002
`/scratch/stefan/7769621/working/3D/1002' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(N=NC2=C3N=CNC3=NC=N2)CCC(C(=O)[O-])C1(C)C)

`REAL300000040884.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040884.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040884/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040884 none CC1C(N=NC2=C3N=CNC3=NC=N2)CCC(C(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.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, 1, 8, 1, 8, 1, 8, 5, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 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]
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, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17
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, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 32
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040884 none CC1C(N=NC2=C3N=CNC3=NC=N2)CCC(C(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.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, 1, 8, 1, 8, 1, 8, 5, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 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]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 3, 3, 1, 1, 1, 2, 2, 2, 1, 1, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 17
rigid atoms, others: [0, 1, 2, 3, 36, 33, 38, 32, 34, 14, 15, 16, 17, 35, 20, 21, 22, 26, 27, 37, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 40, 18, 19, 39, 41, 23, 24, 25, 28, 29, 30])
total number of confs: 41
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040884 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040884
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040884/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040884
Building REAL300000040885
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040885'
/scratch/stefan/7769621/working/building/REAL300000040885 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040885

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040885/0 /scratch/stefan/7769621/working/building/REAL300000040885 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1003)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1003
`/scratch/stefan/7769621/working/3D/1003' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(C)=NNC2=C3N=CN=C3N=C[N-]2)=CC=C1OCCCC(=O)[O-])

`REAL300000040885.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040885.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040885/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040885 none COC1=CC(C(C)=NNC2=C3N=CN=C3N=C[N-]2)=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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 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]
dock color type numbers: [7, 3, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [76, 41, 41, 41, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 129, 175, 179, 201, 201, 201, 76, 76, 76, 41, 13, 13, 13, 2, 1, 1, 41, 41, 175, 175, 179, 179, 201, 201] 201
rigid atoms, others: [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, 35, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 625
number of broken/clashed sets: 32
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040885 none COC1=CC(C(C)=NNC2=C3N=CN=C3N=C[N-]2)=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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 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]
dock color type numbers: [7, 3, 7, 7, 7, 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]
0  hydrogens 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, 6, 25, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 9, 31, 33, 46, 65, 65, 3, 3, 3, 1, 7, 7, 7, 25, 41, 41, 1, 1, 31, 31, 33, 33, 46, 46] 201
rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 18, 19, 20, 21, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45])
total number of confs: 356
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040885 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040885
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040885/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040885
Building REAL300000040886
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040886'
/scratch/stefan/7769621/working/building/REAL300000040886 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040886

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040886/0 /scratch/stefan/7769621/working/building/REAL300000040886 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1004)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1004
`/scratch/stefan/7769621/working/3D/1004' -> `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(N=NC2=C3N=CNC3=NC=N2)C1)

`REAL300000040886.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040886.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040886/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040886 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=C3N=CNC3=NC=N2)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', '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, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 3, 7, 3, 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: [33, 25, 33, 25, 25, 62, 62, 62, 62, 62, 62, 25, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 62, 62, 62, 62, 25, 25, 25, 1, 1, 1, 25, 25] 62
rigid atoms, others: [32, 33, 34, 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, 35, 36])
total number of confs: 145
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: REAL300000040886 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=C3N=CNC3=NC=N2)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', '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, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [17, 11, 17, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 34, 34, 62, 62, 62, 62, 62, 62, 62, 62, 11, 1, 1, 1, 1, 11, 11, 11, 62, 62, 62, 11, 11] 62
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 125
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040886 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=C3N=CNC3=NC=N2)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', '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, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 11, 11, 11, 11, 11, 11, 1, 1, 1, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 1, 11, 11, 11, 11, 1, 1, 1, 25, 25, 25, 1, 1] 62
rigid atoms, others: [1, 3, 4, 11, 12, 13, 35, 24, 36, 29, 30, 31] set([0, 2, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 32, 33, 34])
total number of confs: 50
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040886 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040886
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040886/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040886
Building REAL300000040887
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040887'
/scratch/stefan/7769621/working/building/REAL300000040887 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040887

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040887/0 /scratch/stefan/7769621/working/building/REAL300000040887 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1005)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1005
`/scratch/stefan/7769621/working/3D/1005' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC1=C2N=CN=C2NC=N1)

`REAL300000040887.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040887.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040887/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040887 none O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC1=C2N=CN=C2NC=N1 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', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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, 5, 5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 17, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17
rigid atoms, others: [34, 35, 36, 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])
total number of confs: 33
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040887 none O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC1=C2N=CN=C2NC=N1 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', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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, 5, 5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17] 17
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32] set([33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 21, 22, 23])
total number of confs: 29
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040887 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040887
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040887/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040887
Building REAL300000040888
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040888'
/scratch/stefan/7769621/working/building/REAL300000040888 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040888

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040888/0 /scratch/stefan/7769621/working/building/REAL300000040888 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1006)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1006
`/scratch/stefan/7769621/working/3D/1006' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2N=CN=C2NC=N1)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1)

`REAL300000040888.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040888.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040888/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040888 none CC(=NNC1=C2N=CN=C2NC=N1)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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 6, 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, 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]
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: [9, 1, 9, 9, 43, 73, 73, 73, 73, 73, 73, 73, 73, 1, 1, 1, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 43, 73, 73, 73, 2, 2, 1, 1, 2, 2, 2, 1] 79
rigid atoms, others: [1, 36, 37, 41, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40])
total number of confs: 177
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040888 none CC(=NNC1=C2N=CN=C2NC=N1)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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 6, 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, 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]
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: [40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 73, 73, 79, 79, 79, 73, 73, 73, 73, 73, 73, 73, 73, 41, 41, 41, 10, 1, 1, 1, 79, 79, 73, 73, 73, 73, 73, 73] 79
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: 154
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040888 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040888
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040888/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040888
Building REAL300000040889
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040889'
/scratch/stefan/7769621/working/building/REAL300000040889 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040889

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040889/0 /scratch/stefan/7769621/working/building/REAL300000040889 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1007)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1007
`/scratch/stefan/7769621/working/3D/1007' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=C2N=CN=C2NC=N1)

`REAL300000040889.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040889.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040889/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040889 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=C2N=CN=C2NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 59, 59, 59, 59, 59, 59, 59, 59, 33, 33, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59, 59, 33, 8, 1, 1, 1] 59
rigid atoms, others: [33, 34, 35, 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])
total number of confs: 92
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040889 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=C2N=CN=C2NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 12, 12, 42, 59, 59, 59, 59, 59, 59, 59, 59, 2, 2, 2, 1, 2, 2, 2, 1, 12, 42, 59, 59, 59] 59
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 26, 30] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35])
total number of confs: 151
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040889 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040889
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040889/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040889
Building REAL300000040890
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040890'
/scratch/stefan/7769621/working/building/REAL300000040890 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040890

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040890/0 /scratch/stefan/7769621/working/building/REAL300000040890 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1008)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1008
`/scratch/stefan/7769621/working/3D/1008' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(C=NNC2=C3N=CN=C3NC=N2)=C1Cl)

`REAL300000040890.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040890.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040890/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040890 none O=C([O-])C1=CC=CC(C=NNC2=C3N=CN=C3NC=N2)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 16, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 29, 24, 24, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 24, 8, 1, 1, 1] 29
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 49
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040890 none O=C([O-])C1=CC=CC(C=NNC2=C3N=CN=C3NC=N2)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 16, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 18, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 6, 18, 29, 29, 29] 29
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29])
total number of confs: 69
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040890 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040890
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040890/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040890
Building REAL300000040891
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040891'
/scratch/stefan/7769621/working/building/REAL300000040891 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040891

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040891/0 /scratch/stefan/7769621/working/building/REAL300000040891 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1009)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1009
`/scratch/stefan/7769621/working/3D/1009' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC1=C2N=CN=C2NC=N1)

`REAL300000040891.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040891.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040891/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040891 none O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC1=C2N=CN=C2NC=N1 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', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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, 5, 5, 5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 18
rigid atoms, others: [37, 38, 39, 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])
total number of confs: 32
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040891 none O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC1=C2N=CN=C2NC=N1 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', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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, 5, 5, 5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 17, 17, 17] 18
rigid atoms, others: [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] set([36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 23, 24])
total number of confs: 31
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040891 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040891
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040891/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040891
Building REAL300000040892
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040892'
/scratch/stefan/7769621/working/building/REAL300000040892 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040892

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040892/0 /scratch/stefan/7769621/working/building/REAL300000040892 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1010)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1010
`/scratch/stefan/7769621/working/3D/1010' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C(OC1=CC=CC(C=NNC2=C3N=CN=C3N=C[N-]2)=C1)C1=CC=CC=C1)

`REAL300000040892.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040892.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040892/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040892 none O=C([O-])C(OC1=CC=CC(C=NNC2=C3N=CN=C3N=C[N-]2)=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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', '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: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 46, 46, 46, 46, 46, 70, 70, 154, 201, 201, 201, 201, 201, 201, 201, 201, 46, 1, 1, 1, 1, 1, 1, 3, 46, 46, 46, 70, 154, 201, 201, 46, 1, 1, 1, 1, 1] 201
rigid atoms, others: [3, 38, 39, 40, 41, 42, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 462
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040892 none O=C([O-])C(OC1=CC=CC(C=NNC2=C3N=CN=C3N=C[N-]2)=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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', '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: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 192, 201, 95, 23, 23, 23, 23, 23, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 192, 201, 201, 201, 201, 201, 192, 23, 23, 23, 12, 4, 1, 1, 23, 201, 201, 201, 201, 201] 201
rigid atoms, others: [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, 34, 37, 38, 39, 40, 41, 42])
total number of confs: 639
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040892 none O=C([O-])C(OC1=CC=CC(C=NNC2=C3N=CN=C3N=C[N-]2)=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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', '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: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 34, 49, 11, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 24, 24, 24, 24, 24, 24, 24, 23, 1, 34, 46, 46, 46, 46, 46, 34, 1, 1, 1, 5, 18, 24, 24, 1, 46, 46, 46, 46, 46] 201
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 22, 37, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 249
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040892 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040892/1 /scratch/stefan/7769621/working/building/REAL300000040892 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 1011)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1011
`/scratch/stefan/7769621/working/3D/1011' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C(OC1=CC=CC(CN=NC2=C3N=CNC3=NC=N2)=C1)C1=CC=CC=C1)

`REAL300000040892.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040892.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040892/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040892 none O=C([O-])C(OC1=CC=CC(CN=NC2=C3N=CNC3=NC=N2)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', '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: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 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: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 3, 1, 3, 6, 24, 24, 6, 24, 24, 85, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 24, 1, 1, 1, 1, 1, 1, 3, 24, 24, 9, 85, 85, 201, 201, 201, 24, 1, 1, 1, 1, 1] 201
rigid atoms, others: [3, 39, 40, 41, 42, 43, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 478
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: REAL300000040892 none O=C([O-])C(OC1=CC=CC(CN=NC2=C3N=CNC3=NC=N2)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', '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: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 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: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 129, 40, 40, 40, 40, 40, 10, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 201, 201, 201, 201, 201, 201, 201, 40, 40, 40, 9, 10, 1, 1, 1, 40, 201, 201, 201, 201, 201] 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, 40, 41, 42, 43])
total number of confs: 555
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040892 none O=C([O-])C(OC1=CC=CC(CN=NC2=C3N=CNC3=NC=N2)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', '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: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 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: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 23, 23, 9, 1, 1, 1, 1, 1, 1, 1, 6, 39, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 23, 24, 24, 23, 24, 24, 23, 1, 1, 1, 6, 6, 40, 40, 40, 1, 24, 24, 23, 24, 24] 201
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 22, 38, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43])
total number of confs: 134
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040892 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040892
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040892/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040892/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040892
Building REAL300000040893
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040893'
/scratch/stefan/7769621/working/building/REAL300000040893 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040893

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040893/0 /scratch/stefan/7769621/working/building/REAL300000040893 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1012)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1012
`/scratch/stefan/7769621/working/3D/1012' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)C=C1F)

`REAL300000040893.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040893.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040893/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040893 none O=C([O-])C1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)C=C1F NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 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]
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, 125, 126, 125, 125, 125, 62, 62, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 125, 125, 125, 125, 125, 62, 12, 1, 1, 125] 126
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 28])
total number of confs: 192
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040893 none O=C([O-])C1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)C=C1F NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 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]
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, 3, 1, 1, 1, 1, 1, 12, 12, 55, 125, 125, 125, 125, 125, 125, 125, 125, 1, 1, 1, 1, 1, 12, 55, 125, 125, 1] 126
rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27])
total number of confs: 239
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040893 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040893
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040893/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040893
Building REAL300000040894
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040894'
/scratch/stefan/7769621/working/building/REAL300000040894 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040894

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040894/0 /scratch/stefan/7769621/working/building/REAL300000040894 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1013)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1013
`/scratch/stefan/7769621/working/3D/1013' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2N=CN=C2NC=N1)C1=CC(C(=O)[O-])=CC=C1OC(C)C)

`REAL300000040894.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040894.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040894/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040894 none CC(=NNC1=C2N=CN=C2NC=N1)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 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, 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]
0  hydrogens 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, 56, 157, 157, 157, 157, 157, 157, 157, 157, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 21, 21, 9, 9, 9, 56, 157, 157, 157, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21] 201
rigid atoms, others: [1, 34, 35, 33, 13, 14, 15, 16, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 339
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040894 none CC(=NNC1=C2N=CN=C2NC=N1)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 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, 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]
0  hydrogens 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, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 157, 157, 157, 157, 157, 157, 157, 157, 157, 201, 201, 201, 39, 39, 39, 9, 1, 1, 1, 157, 157, 157, 201, 201, 201, 201, 201, 201, 201] 201
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])
total number of confs: 293
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040894 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040894
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040894/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040894
Building REAL300000040895
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040895'
/scratch/stefan/7769621/working/building/REAL300000040895 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040895

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040895/0 /scratch/stefan/7769621/working/building/REAL300000040895 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1014)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1014
`/scratch/stefan/7769621/working/3D/1014' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC2=C1C(=NNC1=C3N=CN=C3NC=N1)CC2)

`REAL300000040895.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040895.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040895/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040895 none O=C([O-])C1=CC=CC2=C1C(=NNC1=C3N=CN=C3NC=N1)CC2 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.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', '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, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 5, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [25, 24, 25, 24, 24, 24, 24, 24, 24, 24, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 12, 1, 1, 1, 24, 24, 24, 24] 25
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 33, 32, 21, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 51
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040895 none O=C([O-])C1=CC=CC2=C1C(=NNC1=C3N=CN=C3NC=N1)CC2 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.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', '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, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 5, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 7, 24, 24, 24, 1, 1, 1, 1] 25
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 33, 30, 31] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29])
total number of confs: 43
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040895 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040895
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040895/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040895
Building REAL300000040896
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040896'
/scratch/stefan/7769621/working/building/REAL300000040896 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040896

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040896/0 /scratch/stefan/7769621/working/building/REAL300000040896 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1015)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1015
`/scratch/stefan/7769621/working/3D/1015' -> `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=NNC3=C4N=CN=C4NC=N3)C=C2)C=C1)

`REAL300000040896.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040896.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040896/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040896 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=C4N=CN=C4NC=N3)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [39, 35, 39, 26, 39, 39, 26, 25, 31, 30, 24, 24, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 39, 39, 39, 39, 31, 31, 24, 8, 1, 1, 1, 30, 30, 39, 39] 39
rigid atoms, others: [33, 34, 35, 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, 36, 37, 38, 39])
total number of confs: 165
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: REAL300000040896 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=C4N=CN=C4NC=N3)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 25, 37, 37, 37, 37, 37, 37, 37, 36, 1, 1, 3, 3, 3, 3, 1, 1, 6, 24, 37, 37, 37, 1, 1, 3, 3] 39
rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 23, 24, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 31, 32, 33, 34, 35, 38, 39])
total number of confs: 94
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040896 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=C4N=CN=C4NC=N3)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 1, 1, 8, 9, 27, 39, 39, 39, 39, 39, 39, 39, 39, 3, 3, 1, 1, 1, 1, 3, 3, 8, 27, 39, 39, 39, 3, 3, 1, 1] 39
rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 25, 26, 27, 28, 39] 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])
total number of confs: 98
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040896 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040896
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040896/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040896
Building REAL300000040897
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040897'
/scratch/stefan/7769621/working/building/REAL300000040897 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040897

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040897/0 /scratch/stefan/7769621/working/building/REAL300000040897 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1016)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1016
`/scratch/stefan/7769621/working/3D/1016' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2NC=C(C=NNC3=C4N=CN=C4NC=N3)C2=C1)

`REAL300000040897.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040897.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040897/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040897 none O=C([O-])C1=CC=C2NC=C(C=NNC3=C4N=CN=C4NC=N3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 6, 7, 7, 6, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 29, 29, 25, 25, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 25, 9, 1, 1, 1, 29] 29
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 50
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040897 none O=C([O-])C1=CC=C2NC=C(C=NNC3=C4N=CN=C4NC=N3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 6, 7, 7, 6, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 20, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 7, 20, 29, 29, 29, 1] 29
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 33, 22, 23, 24, 25, 26, 27] set([0, 32, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31])
total number of confs: 65
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040897 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040897
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040897/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040897
Building REAL300000040898
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040898'
/scratch/stefan/7769621/working/building/REAL300000040898 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040898

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040898/0 /scratch/stefan/7769621/working/building/REAL300000040898 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1017)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1017
`/scratch/stefan/7769621/working/3D/1017' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=C3N=CN=C3N=C[N-]2)=CC(Cl)=C1OC(C)C(=O)[O-])

`REAL300000040898.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040898.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040898/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040898 none COC1=CC(C=NNC2=C3N=CN=C3N=C[N-]2)=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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 16, 1, 12, 5, 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, 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]
0  hydrogens 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, 88, 88, 88, 35, 35, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 88, 88, 89, 88, 88, 165, 198, 198, 201, 201, 157, 157, 157, 88, 35, 6, 1, 1, 89, 198, 198, 198, 198] 201
rigid atoms, others: [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, 32, 35, 36, 37, 38, 39])
total number of confs: 565
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040898 none COC1=CC(C=NNC2=C3N=CN=C3N=C[N-]2)=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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 16, 1, 12, 5, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 8, 8, 42, 89, 89, 89, 89, 89, 89, 89, 88, 1, 1, 1, 1, 1, 5, 11, 11, 17, 17, 3, 3, 3, 1, 8, 42, 89, 89, 1, 11, 11, 11, 11] 201
rigid atoms, others: [19, 1, 2, 3, 4, 5, 17, 18, 35, 20, 21, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 36, 37, 38, 39])
total number of confs: 230
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040898 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040898
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040898/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040898
Building REAL300000040899
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040899'
/scratch/stefan/7769621/working/building/REAL300000040899 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040899

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040899/0 /scratch/stefan/7769621/working/building/REAL300000040899 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1018)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1018
`/scratch/stefan/7769621/working/3D/1018' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Cl)SC(C=NNC2=C3N=CN=C3N=C[N-]2)=C1)

`REAL300000040899.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040899.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040899/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040899 none O=C([O-])C1=C(Cl)SC(C=NNC2=C3N=CN=C3N=C[N-]2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
137  conformations in input
total number of sets (complete confs): 137
using faster count positions algorithm for large data
unique positions, atoms: [137, 137, 137, 137, 137, 137, 137, 66, 66, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 137, 66, 12, 1, 1, 137] 137
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 25])
total number of confs: 190
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040899 none O=C([O-])C1=C(Cl)SC(C=NNC2=C3N=CN=C3N=C[N-]2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
137  conformations in input
total number of sets (complete confs): 137
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 13, 13, 67, 137, 137, 137, 137, 137, 137, 137, 137, 1, 13, 67, 137, 137, 1] 137
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 25] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24])
total number of confs: 271
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040899 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040899
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040899/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040899
Building REAL300000040900
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040900'
/scratch/stefan/7769621/working/building/REAL300000040900 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040900

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040900/0 /scratch/stefan/7769621/working/building/REAL300000040900 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1019)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1019
`/scratch/stefan/7769621/working/3D/1019' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2N=CN=C2NC=N1)C1=CC=C(C(=O)[O-])C=C1C)

`REAL300000040900.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040900.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040900/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040900 none CC(=NNC1=C2N=CN=C2NC=N1)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 39, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 9, 39, 53, 53, 53, 1, 1, 1, 2, 2, 2] 53
rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35])
total number of confs: 129
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040900 none CC(=NNC1=C2N=CN=C2NC=N1)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [41, 41, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 53, 53, 53, 53, 53, 53, 53, 53, 53, 42, 42, 42, 10, 1, 1, 1, 53, 53, 53, 53, 53, 53] 53
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: 89
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040900 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040900
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040900/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040900
Building REAL300000040901
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040901'
/scratch/stefan/7769621/working/building/REAL300000040901 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040901

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040901/0 /scratch/stefan/7769621/working/building/REAL300000040901 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1020)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1020
`/scratch/stefan/7769621/working/3D/1020' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C(Cl)C=C1C=NNC1=C2N=CNC2=NC=N1)

`REAL300000040901.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040901.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040901/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040901 none O=C([O-])C1=CN=C(Cl)C=C1C=NNC1=C2N=CNC2=NC=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 16, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [28, 28, 28, 28, 28, 19, 28, 28, 28, 19, 19, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 19, 8, 1, 1, 1] 28
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25])
total number of confs: 62
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040901 none O=C([O-])C1=CN=C(Cl)C=C1C=NNC1=C2N=CNC2=NC=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 16, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 3, 7, 3, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 21, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 4, 21, 28, 28, 28] 28
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28])
total number of confs: 67
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040901 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040901/1 /scratch/stefan/7769621/working/building/REAL300000040901 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 1021)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1021
`/scratch/stefan/7769621/working/3D/1021' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C(Cl)C=C1C=NNC1=C2NC=NC2=NC=N1)

`REAL300000040901.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040901.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040901/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040901 none O=C([O-])C1=CN=C(Cl)C=C1C=NNC1=C2NC=NC2=NC=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 16, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [31, 31, 31, 31, 31, 22, 31, 31, 31, 22, 22, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 22, 7, 1, 1, 1] 31
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25])
total number of confs: 68
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040901 none O=C([O-])C1=CN=C(Cl)C=C1C=NNC1=C2NC=NC2=NC=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 16, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 27, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 12, 27, 31, 31, 31] 31
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28])
total number of confs: 81
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040901 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040901
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040901/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040901/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040901
Building REAL300000040902
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040902'
/scratch/stefan/7769621/working/building/REAL300000040902 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040902

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040902/0 /scratch/stefan/7769621/working/building/REAL300000040902 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1022)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1022
`/scratch/stefan/7769621/working/3D/1022' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C2=CC=C(C=NNC3=C4N=CN=C4N=C[N-]3)O2)=CC=C1O)

`REAL300000040902.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040902.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040902/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040902 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=C4N=CN=C4N=C[N-]3)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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, 87, 87, 87, 87, 51, 51, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 87, 201, 201, 201, 201, 201, 87, 87, 51, 10, 1, 1, 201, 201, 402] 402
rigid atoms, others: [32, 33, 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, 34, 35, 36])
total number of confs: 684
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: REAL300000040902 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=C4N=CN=C4N=C[N-]3)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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: [25, 12, 25, 12, 12, 1, 1, 1, 1, 1, 1, 8, 8, 39, 87, 87, 87, 87, 87, 87, 87, 87, 1, 12, 12, 12, 12, 12, 1, 1, 8, 39, 87, 87, 12, 12, 24] 402
rigid atoms, others: [5, 6, 7, 8, 9, 10, 22, 28, 29] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040902 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=C4N=CN=C4N=C[N-]3)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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, 12, 12, 12, 12, 37, 37, 126, 201, 201, 201, 201, 201, 201, 201, 201, 12, 1, 1, 1, 1, 1, 12, 12, 37, 126, 201, 201, 1, 1, 2] 402
rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 23, 24, 25, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 36])
total number of confs: 442
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040902 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040902
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040902/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040902
Building REAL300000040903
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040903'
/scratch/stefan/7769621/working/building/REAL300000040903 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040903

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040903/0 /scratch/stefan/7769621/working/building/REAL300000040903 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1023)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1023
`/scratch/stefan/7769621/working/3D/1023' -> `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=NNC1=C2N=CN=C2NC=N1)

`REAL300000040903.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040903.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040903/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040903 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=C2N=CN=C2NC=N1 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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 14, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 8, 1, 1, 1] 15
rigid atoms, others: [35, 36, 37, 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])
total number of confs: 28
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040903 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=C2N=CN=C2NC=N1 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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 4, 4, 10, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2, 1, 1, 1, 4, 10, 15, 15, 15] 15
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 10, 11, 12, 30, 31] set([0, 2, 8, 9, 13, 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: 43
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040903 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040903/1 /scratch/stefan/7769621/working/building/REAL300000040903 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 1024)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1024
`/scratch/stefan/7769621/working/3D/1024' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC=C(C(=O)[O-])C=C1C=[NH+][N-]C1=C2N=CN=C2NC=N1)

`REAL300000040903.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040903.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040903/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040903 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=[NH+][N-]C1=C2N=CN=C2NC=N1 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.pl3', 'H', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 6, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 30, 30, 30, 30, 30, 16, 16, 9, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 16, 1, 1, 1] 30
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: 51
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040903 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=[NH+][N-]C1=C2N=CN=C2NC=N1 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.pl3', 'H', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 6, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 2, 2, 1, 1, 1, 13, 13, 13, 20, 30, 30, 30, 30, 30, 30, 30, 30, 3, 3, 3, 3, 3, 3, 1, 1, 1, 13, 30, 30, 30] 30
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 10, 11, 12, 33, 31] set([0, 2, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37])
total number of confs: 76
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040903 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040903
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040903/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040903/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040903
Building REAL300000040904
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040904'
/scratch/stefan/7769621/working/building/REAL300000040904 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040904

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040904/0 /scratch/stefan/7769621/working/building/REAL300000040904 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1025)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1025
`/scratch/stefan/7769621/working/3D/1025' -> `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=NNC3=C4N=CN=C4NC=N3)S2)C=C1)

`REAL300000040904.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040904.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040904/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040904 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=C4N=CN=C4NC=N3)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'S.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 61, 103, 61, 103, 103, 61, 61, 61, 61, 43, 43, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 61, 103, 103, 103, 103, 61, 61, 43, 10, 1, 1, 1, 103, 103] 103
rigid atoms, others: [32, 33, 34, 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, 35, 36])
total number of confs: 436
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: REAL300000040904 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=C4N=CN=C4NC=N3)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'S.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 1, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 37, 61, 61, 61, 61, 61, 61, 61, 61, 1, 7, 7, 7, 7, 1, 1, 7, 37, 61, 61, 61, 7, 7] 103
rigid atoms, others: [6, 7, 8, 9, 10, 11, 23, 28, 29] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 154
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040904 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=C4N=CN=C4NC=N3)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'S.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 8, 8, 8, 34, 34, 72, 87, 87, 87, 87, 87, 87, 87, 87, 8, 1, 1, 1, 1, 8, 8, 34, 72, 87, 87, 87, 1, 1] 87
rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 24, 25, 26, 27, 36] 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: 211
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040904 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040904
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040904/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040904
Building REAL300000040905
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040905'
/scratch/stefan/7769621/working/building/REAL300000040905 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040905

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040905/0 /scratch/stefan/7769621/working/building/REAL300000040905 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1026)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1026
`/scratch/stefan/7769621/working/3D/1026' -> `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=NNC3=C4N=CN=C4NC=N3)S2)=C1)

`REAL300000040905.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040905.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040905/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040905 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=C4N=CN=C4NC=N3)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'S.3', 'C.ar', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
175  conformations in input
total number of sets (complete confs): 175
using faster count positions algorithm for large data
unique positions, atoms: [175, 175, 175, 175, 175, 175, 175, 93, 93, 93, 93, 49, 49, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 93, 175, 175, 175, 175, 93, 93, 49, 10, 1, 1, 1, 175] 175
rigid atoms, others: [33, 34, 35, 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, 36])
total number of confs: 263
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: REAL300000040905 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=C4N=CN=C4NC=N3)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'S.3', 'C.ar', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
175  conformations in input
total number of sets (complete confs): 175
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 13, 12, 13, 13, 1, 1, 1, 1, 1, 1, 8, 8, 37, 93, 93, 93, 93, 93, 93, 93, 93, 1, 13, 12, 13, 13, 1, 1, 8, 37, 93, 93, 93, 13] 175
rigid atoms, others: [7, 8, 9, 10, 11, 12, 24, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36])
total number of confs: 182
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040905 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=C4N=CN=C4NC=N3)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'S.3', 'C.ar', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
175  conformations in input
total number of sets (complete confs): 175
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 12, 13, 50, 50, 133, 175, 175, 175, 175, 175, 175, 175, 175, 13, 1, 1, 1, 1, 13, 13, 50, 133, 175, 175, 175, 1] 175
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28, 36] set([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: 407
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040905 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040905
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040905/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040905
Building REAL300000040906
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040906'
/scratch/stefan/7769621/working/building/REAL300000040906 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040906

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040906/0 /scratch/stefan/7769621/working/building/REAL300000040906 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1027)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1027
`/scratch/stefan/7769621/working/3D/1027' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC(C(=O)[O-])=C(C=NNC2=C3N=CN=C3NC=N2)S1)

`REAL300000040906.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040906.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040906/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040906 none CCC1=CC(C(=O)[O-])=C(C=NNC2=C3N=CN=C3NC=N2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 45, 45, 45, 43, 46, 49, 49, 36, 36, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 75, 75, 75, 74, 75, 45, 36, 8, 1, 1, 1] 75
rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 255
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040906 none CCC1=CC(C(=O)[O-])=C(C=NNC2=C3N=CN=C3NC=N2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 46, 46, 46, 46, 46, 46, 46, 46, 1, 8, 8, 8, 8, 8, 1, 3, 25, 46, 46, 46] 75
rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 21, 27] set([0, 6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32])
total number of confs: 120
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040906 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040906
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040906/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040906
Building REAL300000040907
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040907'
/scratch/stefan/7769621/working/building/REAL300000040907 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040907

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040907/0 /scratch/stefan/7769621/working/building/REAL300000040907 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1028)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1028
`/scratch/stefan/7769621/working/3D/1028' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=NNC1=C2N=CN=C2NC=N1)

`REAL300000040907.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040907.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040907/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040907 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=C2N=CN=C2NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [108, 108, 108, 108, 108, 108, 108, 108, 108, 108, 42, 42, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 108, 108, 108, 42, 8, 1, 1, 1] 108
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: 150
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040907 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=C2N=CN=C2NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 63, 108, 108, 108, 108, 108, 108, 108, 108, 4, 4, 4, 1, 1, 1, 12, 63, 108, 108, 108] 108
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31])
total number of confs: 225
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040907 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040907
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040907/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040907
Building REAL300000040908
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040908'
/scratch/stefan/7769621/working/building/REAL300000040908 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300000040908

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040908/0 /scratch/stefan/7769621/working/building/REAL300000040908 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1029)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1029
`/scratch/stefan/7769621/working/3D/1029' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2SC=C(CN=NC3=C4N=CNC4=NC=N3)C2=C1)

`REAL300000040908.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040908.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040908/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040908 none O=C([O-])C1=CC=C2SC=C(CN=NC3=C4N=CNC4=NC=N3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
104  conformations in input
total number of sets (complete confs): 104
using faster count positions algorithm for large data
unique positions, atoms: [104, 104, 104, 104, 104, 104, 104, 104, 104, 45, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 104, 104, 104, 104, 104, 45, 45, 1, 1, 1, 104] 104
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 230
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040908 none O=C([O-])C1=CC=C2SC=C(CN=NC3=C4N=CNC4=NC=N3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
104  conformations in input
total number of sets (complete confs): 104
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 51, 51, 104, 104, 104, 104, 104, 104, 104, 104, 1, 1, 1, 1, 1, 8, 8, 104, 104, 104, 1] 104
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31])
total number of confs: 166
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040908 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040908/1 /scratch/stefan/7769621/working/building/REAL300000040908 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 1030)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1030
`/scratch/stefan/7769621/working/3D/1030' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2SC=C(C=NNC3=C4N=CNC4=NC=N3)C2=C1)

`REAL300000040908.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040908.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040908/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040908 none O=C([O-])C1=CC=C2SC=C(C=NNC3=C4N=CNC4=NC=N3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 3, 7, 3, 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, 29, 29, 29, 24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 24, 6, 1, 1, 1, 29] 29
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 44
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040908 none O=C([O-])C1=CC=C2SC=C(C=NNC3=C4N=CNC4=NC=N3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 3, 7, 3, 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, 1, 1, 1, 6, 6, 16, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 6, 16, 29, 29, 29, 1] 29
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31])
total number of confs: 65
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040908 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `2'
/scratch/stefan/7769621/working/building/REAL300000040908/2 /scratch/stefan/7769621/working/building/REAL300000040908 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 2 (index: 1031)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1031
`/scratch/stefan/7769621/working/3D/1031' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2SC=C(C=NNC3=C4NC=NC4=NC=N3)C2=C1)

`REAL300000040908.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300000040908.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040908/2/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`2.mol2' -> `2.mol2.original'
`output.mol2' -> `2.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040908 none O=C([O-])C1=CC=C2SC=C(C=NNC3=C4NC=NC4=NC=N3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 3, 7, 3, 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, 17, 17, 17, 11, 11, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 11, 7, 1, 1, 1, 17] 17
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 31
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040908 none O=C([O-])C1=CC=C2SC=C(C=NNC3=C4NC=NC4=NC=N3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 3, 7, 3, 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, 1, 1, 1, 10, 10, 14, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 10, 14, 17, 17, 17, 1] 17
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31])
total number of confs: 43
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040908 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040908
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
2: /scratch/stefan/7769621/working/building/REAL300000040908/2.*
1: /scratch/stefan/7769621/working/building/REAL300000040908/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040908/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040908
Building REAL300000040909
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040909'
/scratch/stefan/7769621/working/building/REAL300000040909 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040909

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040909/0 /scratch/stefan/7769621/working/building/REAL300000040909 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1032)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1032
`/scratch/stefan/7769621/working/3D/1032' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2CCCC(=NNC3=C4N=CN=C4NC=N3)C2=C1)

`REAL300000040909.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040909.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040909/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040909 none O=C([O-])C1=CN=C2CCCC(=NNC3=C4N=CN=C4NC=N3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 17] 17
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35])
total number of confs: 33
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040909 none O=C([O-])C1=CN=C2CCCC(=NNC3=C4N=CN=C4NC=N3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 1, 1, 1, 1, 1, 7, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 1] 17
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 35, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 32, 2, 34, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31])
total number of confs: 33
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040909 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040909
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040909/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040909
Building REAL300000040910
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040910'
/scratch/stefan/7769621/working/building/REAL300000040910 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040910

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040910/0 /scratch/stefan/7769621/working/building/REAL300000040910 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1033)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1033
`/scratch/stefan/7769621/working/3D/1033' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(Br)C(C=NNC2=C3N=CN=C3N=C[N-]2)=C1)

`REAL300000040910.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040910.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040910/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040910 none O=C([O-])C1=CC=C(Br)C(C=NNC2=C3N=CN=C3N=C[N-]2)=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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [90, 90, 90, 90, 90, 90, 90, 90, 47, 47, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 90, 90, 90, 47, 13, 1, 1, 90] 90
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 28])
total number of confs: 135
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040910 none O=C([O-])C1=CC=C(Br)C(C=NNC2=C3N=CN=C3N=C[N-]2)=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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 11, 11, 61, 90, 90, 90, 90, 90, 90, 90, 90, 1, 1, 1, 11, 61, 90, 90, 1] 90
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 28] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27])
total number of confs: 198
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040910 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040910
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040910/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040910
Building REAL300000040911
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040911'
/scratch/stefan/7769621/working/building/REAL300000040911 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040911

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040911/0 /scratch/stefan/7769621/working/building/REAL300000040911 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1034)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1034
`/scratch/stefan/7769621/working/3D/1034' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=C3N=CN=C3NC=N2)=CC=C1C(=O)[O-])

`REAL300000040911.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040911.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040911/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040911 none COC1=CC(C=NNC2=C3N=CN=C3NC=N2)=CC=C1C(=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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 128, 128, 128, 39, 39, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 128, 128, 128, 128, 155, 155, 155, 155, 155, 128, 39, 9, 1, 1, 1, 128, 128] 155
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, 33, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 343
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040911 none COC1=CC(C=NNC2=C3N=CN=C3NC=N2)=CC=C1C(=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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 12, 12, 48, 128, 128, 128, 128, 128, 128, 128, 128, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 12, 48, 128, 128, 128, 1, 1] 155
rigid atoms, others: [32, 1, 2, 3, 4, 5, 33, 17, 18, 19, 20, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31])
total number of confs: 228
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040911 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040911
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040911/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040911
Building REAL300000040912
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040912'
/scratch/stefan/7769621/working/building/REAL300000040912 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040912

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040912/0 /scratch/stefan/7769621/working/building/REAL300000040912 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1035)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1035
`/scratch/stefan/7769621/working/3D/1035' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(F)=C(C=NNC2=C3N=CNC3=NC=N2)C(F)=C1)

`REAL300000040912.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040912.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040912/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040912 none O=C([O-])C1=CC(F)=C(C=NNC2=C3N=CNC3=NC=N2)C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 15, 1, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [29, 24, 29, 24, 29, 29, 29, 24, 23, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 23, 8, 1, 1, 1, 29] 29
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 29])
total number of confs: 85
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040912 none O=C([O-])C1=CC(F)=C(C=NNC2=C3N=CNC3=NC=N2)C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 15, 1, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 3, 7, 3, 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, 1, 7, 7, 22, 28, 29, 29, 29, 28, 28, 28, 28, 1, 1, 1, 1, 7, 22, 29, 29, 29, 1] 29
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 29] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28])
total number of confs: 79
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040912 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040912/1 /scratch/stefan/7769621/working/building/REAL300000040912 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 1036)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1036
`/scratch/stefan/7769621/working/3D/1036' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(F)=C(C=NNC2=C3NC=NC3=NC=N2)C(F)=C1)

`REAL300000040912.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040912.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040912/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040912 none O=C([O-])C1=CC(F)=C(C=NNC2=C3NC=NC3=NC=N2)C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 15, 1, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
6  conformations in input
total number of sets (complete confs): 6
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 4, 1, 1, 1, 6] 6
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 29])
total number of confs: 12
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040912 none O=C([O-])C1=CC(F)=C(C=NNC2=C3NC=NC3=NC=N2)C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 15, 1, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 3, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 5, 6, 6, 6, 6, 1] 6
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 29] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28])
total number of confs: 19
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040912 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040912
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040912/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040912/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040912
Building REAL300000040913
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040913'
/scratch/stefan/7769621/working/building/REAL300000040913 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040913

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040913/0 /scratch/stefan/7769621/working/building/REAL300000040913 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1037)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1037
`/scratch/stefan/7769621/working/3D/1037' -> `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=NNC2=C3N=CNC3=NC=N2)=C1)

`REAL300000040913.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040913.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040913/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040913 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=C3N=CNC3=NC=N2)=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', 'N.pl3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 7, 6, 7, 6, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
84  conformations in input
total number of sets (complete confs): 84
using faster count positions algorithm for large data
unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 42, 42, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 84, 24, 7, 1, 1, 1, 42] 84
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 30])
total number of confs: 150
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040913 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=C3N=CNC3=NC=N2)=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', 'N.pl3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 7, 6, 7, 6, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
84  conformations in input
total number of sets (complete confs): 84
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 35, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 2, 10, 35, 42, 42, 42, 1] 84
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29])
total number of confs: 102
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040913 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040913
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040913/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040913
Building REAL300000040914
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040914'
/scratch/stefan/7769621/working/building/REAL300000040914 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040914

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040914/0 /scratch/stefan/7769621/working/building/REAL300000040914 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1038)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1038
`/scratch/stefan/7769621/working/3D/1038' -> `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=NNC3=C4N=CN=C4N=C[N-]3)C=C2)O1)

`REAL300000040914.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040914.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040914/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040914 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=C4N=CN=C4N=C[N-]3)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'O.3', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
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, 137, 127, 126, 93, 126, 126, 53, 53, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 126, 126, 201, 201, 201, 137, 137, 126, 126, 53, 10, 1, 1, 127, 127] 201
rigid atoms, others: [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, 35, 38, 39])
total number of confs: 488
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040914 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=C4N=CN=C4N=C[N-]3)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'O.3', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens 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, 13, 4, 2, 1, 1, 1, 1, 1, 1, 12, 12, 57, 127, 127, 127, 127, 127, 127, 127, 127, 1, 1, 13, 13, 13, 4, 4, 1, 1, 12, 57, 127, 127, 1, 1] 201
rigid atoms, others: [32, 33, 38, 39, 8, 9, 10, 11, 12, 13, 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, 34, 35, 36, 37])
total number of confs: 264
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040914 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=C4N=CN=C4N=C[N-]3)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'O.3', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens 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, 8, 12, 13, 13, 13, 13, 49, 49, 162, 201, 201, 201, 201, 201, 201, 201, 201, 13, 13, 1, 1, 1, 8, 8, 13, 13, 49, 162, 201, 201, 13, 13] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 509
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040914 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040914/1 /scratch/stefan/7769621/working/building/REAL300000040914 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 1039)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1039
`/scratch/stefan/7769621/working/3D/1039' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(COC2=CC=C(CN=NC3=C4N=CNC4=NC=N3)C=C2)O1)

`REAL300000040914.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040914.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040914/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040914 none O=C([O-])C1=CC=C(COC2=CC=C(CN=NC3=C4N=CNC4=NC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.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, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 106, 106, 39, 23, 106, 106, 23, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 106, 106, 201, 201, 201, 106, 106, 106, 106, 22, 23, 1, 1, 1, 106, 106] 201
rigid atoms, others: [36, 37, 38, 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, 39, 40])
total number of confs: 574
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: REAL300000040914 none O=C([O-])C1=CC=C(COC2=CC=C(CN=NC3=C4N=CNC4=NC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.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, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 7, 8, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 65, 65, 106, 106, 106, 106, 106, 106, 106, 106, 1, 1, 7, 7, 7, 1, 1, 1, 1, 9, 9, 106, 106, 106, 1, 1] 201
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 40, 39, 25, 26, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 34, 35, 36, 37, 38])
total number of confs: 184
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040914 none O=C([O-])C1=CC=C(COC2=CC=C(CN=NC3=C4N=CNC4=NC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.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, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 45, 174, 174, 201, 201, 201, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 7, 7, 7, 7, 45, 45, 201, 201, 201, 7, 7] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 384
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040914 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040914
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040914/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040914/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040914
Building REAL300000040915
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040915'
/scratch/stefan/7769621/working/building/REAL300000040915 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300000040915

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040915/0 /scratch/stefan/7769621/working/building/REAL300000040915 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1040)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1040
`/scratch/stefan/7769621/working/3D/1040' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC=CC=C2C(CN=NC2=C3N=CNC3=NC=N2)=C1O)

`REAL300000040915.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040915.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040915/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040915 none O=C([O-])C1=CC2=CC=CC=C2C(CN=NC2=C3N=CNC3=NC=N2)=C1O 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.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', '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, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
186  conformations in input
total number of sets (complete confs): 186
using faster count positions algorithm for large data
unique positions, atoms: [93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 41, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 93, 93, 93, 40, 41, 1, 1, 1, 186] 186
rigid atoms, others: [33, 34, 35, 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, 36])
total number of confs: 384
number of broken/clashed sets: 107
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040915 none O=C([O-])C1=CC2=CC=CC=C2C(CN=NC2=C3N=CNC3=NC=N2)=C1O 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.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', '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, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
186  conformations in input
total number of sets (complete confs): 186
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 46, 46, 93, 93, 93, 93, 93, 93, 93, 93, 1, 1, 1, 1, 1, 1, 1, 7, 7, 93, 93, 93, 2] 186
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30] set([0, 32, 2, 34, 36, 35, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31])
total number of confs: 149
number of broken/clashed sets: 107
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040915 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040915/1 /scratch/stefan/7769621/working/building/REAL300000040915 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 1041)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1041
`/scratch/stefan/7769621/working/3D/1041' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=C3N=CNC3=NC=N2)=C1O)

`REAL300000040915.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040915.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040915/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040915 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=C3N=CNC3=NC=N2)=C1O 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.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 24, 23, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49, 23, 8, 1, 1, 1, 98] 98
rigid atoms, others: [33, 34, 35, 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, 36])
total number of confs: 169
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040915 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=C3N=CNC3=NC=N2)=C1O 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.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 38, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 9, 38, 49, 49, 49, 2] 98
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30] set([0, 32, 2, 34, 36, 35, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31])
total number of confs: 119
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040915 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `2'
/scratch/stefan/7769621/working/building/REAL300000040915/2 /scratch/stefan/7769621/working/building/REAL300000040915 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 2 (index: 1042)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1042
`/scratch/stefan/7769621/working/3D/1042' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=C3NC=NC3=NC=N2)=C1O)

`REAL300000040915.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300000040915.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040915/2/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`2.mol2' -> `2.mol2.original'
`output.mol2' -> `2.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040915 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=C3NC=NC3=NC=N2)=C1O 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.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 4, 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, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 17, 4, 1, 1, 1, 58] 58
rigid atoms, others: [33, 34, 35, 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, 36])
total number of confs: 100
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040915 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=C3NC=NC3=NC=N2)=C1O 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.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 4, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 26, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 11, 26, 29, 29, 29, 2] 58
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30] set([0, 32, 2, 34, 36, 35, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31])
total number of confs: 79
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040915 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040915
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
2: /scratch/stefan/7769621/working/building/REAL300000040915/2.*
1: /scratch/stefan/7769621/working/building/REAL300000040915/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040915/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040915
Building REAL300000040916
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040916'
/scratch/stefan/7769621/working/building/REAL300000040916 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040916

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040916/0 /scratch/stefan/7769621/working/building/REAL300000040916 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1043)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1043
`/scratch/stefan/7769621/working/3D/1043' -> `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=NNC3=C4N=CN=C4N=C[N-]3)C=C2)=C1)

`REAL300000040916.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040916.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040916/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040916 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=C4N=CN=C4N=C[N-]3)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 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]
0  hydrogens need rotated
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, 133, 133, 133, 133, 133, 72, 70, 78, 78, 44, 44, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 78, 78, 133, 201, 201, 133, 133, 133, 78, 78, 44, 10, 1, 1, 78, 78, 133] 201
rigid atoms, others: [37, 38, 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, 39, 40, 41])
total number of confs: 667
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: REAL300000040916 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=C4N=CN=C4N=C[N-]3)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 5, 13, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 8, 8, 50, 79, 79, 79, 79, 79, 79, 79, 78, 1, 1, 3, 5, 5, 3, 3, 3, 1, 1, 8, 50, 79, 79, 1, 1, 3] 201
rigid atoms, others: [33, 34, 39, 8, 9, 10, 11, 12, 13, 40, 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, 35, 36, 37, 38, 41])
total number of confs: 206
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040916 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=C4N=CN=C4N=C[N-]3)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 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]
0  hydrogens 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, 2, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 10, 10, 91, 133, 133, 133, 133, 133, 133, 133, 133, 3, 3, 1, 2, 2, 1, 1, 1, 3, 3, 10, 90, 133, 133, 3, 3, 1] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 41, 27, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 311
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040916 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040916/1 /scratch/stefan/7769621/working/building/REAL300000040916 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 1044)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1044
`/scratch/stefan/7769621/working/3D/1044' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CC1=CC=CC(C2=CC=C(CN=NC3=C4N=CNC4=NC=N3)C=C2)=C1)

`REAL300000040916.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040916.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040916/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040916 none O=C([O-])CC1=CC=CC(C2=CC=C(CN=NC3=C4N=CNC4=NC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', '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: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 3, 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, 151, 151, 151, 151, 151, 33, 19, 89, 89, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 89, 89, 151, 201, 201, 151, 151, 151, 89, 88, 18, 19, 1, 1, 1, 89, 89, 151] 201
rigid atoms, others: [37, 38, 39, 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, 40, 41, 42])
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: REAL300000040916 none O=C([O-])CC1=CC=CC(C2=CC=C(CN=NC3=C4N=CNC4=NC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', '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: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 3, 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: [9, 5, 9, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 8, 54, 55, 89, 89, 89, 89, 89, 89, 89, 89, 1, 1, 3, 5, 5, 3, 3, 3, 1, 1, 8, 8, 89, 89, 89, 1, 1, 3] 201
rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 40, 41, 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, 35, 36, 37, 38, 39, 42])
total number of confs: 178
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040916 none O=C([O-])CC1=CC=CC(C2=CC=C(CN=NC3=C4N=CNC4=NC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', '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: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 3, 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: [7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 17, 103, 103, 151, 151, 151, 151, 151, 151, 151, 151, 3, 3, 1, 2, 2, 1, 1, 1, 3, 3, 17, 17, 151, 151, 151, 3, 3, 1] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 42, 27, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 275
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040916 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040916
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040916/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040916/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040916
Building REAL300000040917
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040917'
/scratch/stefan/7769621/working/building/REAL300000040917 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040917

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040917/0 /scratch/stefan/7769621/working/building/REAL300000040917 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1045)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1045
`/scratch/stefan/7769621/working/3D/1045' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NNC2=C3N=CN=C3N=C[N-]2)SC(Cl)=C1)

`REAL300000040917.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040917.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040917/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040917 none O=C([O-])C1=C(C=NNC2=C3N=CN=C3N=C[N-]2)SC(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 14, 1, 16, 1, 7, 6, 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]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [31, 30, 31, 30, 28, 28, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 28, 12, 1, 1, 30] 31
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 25])
total number of confs: 55
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040917 none O=C([O-])C1=C(C=NNC2=C3N=CN=C3N=C[N-]2)SC(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 14, 1, 16, 1, 7, 6, 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]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 3, 3, 14, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 3, 14, 30, 30, 1] 31
rigid atoms, others: [1, 3, 4, 5, 17, 18, 19, 20, 25] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24])
total number of confs: 65
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040917 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040917
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040917/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040917
Building REAL300000040918
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040918'
/scratch/stefan/7769621/working/building/REAL300000040918 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040918

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040918/0 /scratch/stefan/7769621/working/building/REAL300000040918 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1046)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1046
`/scratch/stefan/7769621/working/3D/1046' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC(C=NNC2=C3N=CN=C3N=C[N-]2)=CC=C1OCC(=O)[O-])

`REAL300000040918.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040918.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040918/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040918 none CCOC1=CC(C=NNC2=C3N=CN=C3N=C[N-]2)=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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 12, 5, 1, 11, 11, 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, 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]
0  hydrogens 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, 73, 24, 24, 24, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 117, 181, 195, 195, 94, 94, 94, 94, 94, 24, 8, 2, 1, 1, 25, 25, 181, 181] 201
rigid atoms, others: [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, 33, 36, 37, 38, 39])
total number of confs: 716
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040918 none CCOC1=CC(C=NNC2=C3N=CN=C3N=C[N-]2)=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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 12, 5, 1, 11, 11, 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, 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]
0  hydrogens 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, 6, 6, 21, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 9, 30, 62, 62, 22, 22, 22, 22, 22, 1, 6, 20, 25, 25, 1, 1, 30, 30] 201
rigid atoms, others: [2, 3, 4, 5, 6, 18, 19, 20, 21, 36, 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, 38, 39])
total number of confs: 325
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040918 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040918
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040918/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040918
Building REAL300000040919
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040919'
/scratch/stefan/7769621/working/building/REAL300000040919 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040919

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040919/0 /scratch/stefan/7769621/working/building/REAL300000040919 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1047)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1047
`/scratch/stefan/7769621/working/3D/1047' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC1=C2N=CN=C2NC=N1)

`REAL300000040919.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040919.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040919/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040919 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC1=C2N=CN=C2NC=N1 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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [47, 43, 47, 43, 43, 43, 43, 96, 96, 96, 96, 96, 43, 36, 36, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 96, 96, 96, 96, 96, 96, 96, 96, 96, 43, 36, 10, 1, 1, 1] 96
rigid atoms, others: [38, 39, 40, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 235
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: REAL300000040919 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC1=C2N=CN=C2NC=N1 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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [19, 13, 19, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 23, 23, 74, 96, 96, 96, 96, 96, 96, 96, 96, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 23, 74, 96, 96, 96] 96
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40])
total number of confs: 245
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040919 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC1=C2N=CN=C2NC=N1 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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 1, 4, 4, 20, 43, 43, 43, 43, 43, 43, 43, 43, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 4, 20, 43, 43, 43] 96
rigid atoms, others: [1, 3, 4, 5, 6, 12, 13, 14, 35] set([0, 2, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40])
total number of confs: 111
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040919 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040919
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040919/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040919
Building REAL300000040920
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040920'
/scratch/stefan/7769621/working/building/REAL300000040920 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040920

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040920/0 /scratch/stefan/7769621/working/building/REAL300000040920 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1048)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1048
`/scratch/stefan/7769621/working/3D/1048' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C)C(C=NNC2=C3N=CN=C3NC=N2)=C1C(=O)[O-])

`REAL300000040920.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040920.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040920/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040920 none COC1=CC=C(C)C(C=NNC2=C3N=CN=C3NC=N2)=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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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]
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, 54, 54, 54, 54, 54, 54, 37, 37, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 70, 70, 70, 70, 70, 54, 54, 54, 54, 54, 37, 11, 1, 1, 1] 70
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])
total number of confs: 187
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040920 none COC1=CC=C(C)C(C=NNC2=C3N=CN=C3NC=N2)=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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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]
0  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 24, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1, 3, 3, 3, 4, 3, 1, 1, 2, 2, 2, 4, 24, 54, 54, 54] 70
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 111
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040920 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040920
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040920/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040920
Building REAL300000040921
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040921'
/scratch/stefan/7769621/working/building/REAL300000040921 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040921

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040921/0 /scratch/stefan/7769621/working/building/REAL300000040921 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1049)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1049
`/scratch/stefan/7769621/working/3D/1049' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C2=CC=C(F)C=C2C(C=NNC2=C3N=CN=C3NC=N2)=C1C(=O)[O-])

`REAL300000040921.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040921.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040921/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040921 none CN1C2=CC=C(F)C=C2C(C=NNC2=C3N=CN=C3NC=N2)=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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 28, 23, 23, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 23, 10, 1, 1, 1] 28
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])
total number of confs: 49
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040921 none CN1C2=CC=C(F)C=C2C(C=NNC2=C3N=CN=C3NC=N2)=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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 19, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 3, 3, 2, 2, 2, 1, 1, 1, 4, 19, 28, 28, 28] 28
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 29, 30, 31] set([32, 33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28])
total number of confs: 71
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040921 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040921
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040921/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040921
Building REAL300000040922
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040922'
/scratch/stefan/7769621/working/building/REAL300000040922 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040922

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040922/0 /scratch/stefan/7769621/working/building/REAL300000040922 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1050)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1050
`/scratch/stefan/7769621/working/3D/1050' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2N=CN=C2NC=N1)C1=C(C(=O)[O-])C2=CC=CC=C2S1)

`REAL300000040922.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040922.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040922/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040922 none CC(=NNC1=C2N=CN=C2NC=N1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 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, 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: [7, 1, 7, 7, 26, 58, 58, 58, 58, 58, 58, 58, 58, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 26, 58, 58, 58, 1, 1, 1, 1] 58
rigid atoms, others: [32, 1, 34, 35, 33, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 115
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040922 none CC(=NNC1=C2N=CN=C2NC=N1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [38, 38, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 38, 38, 38, 11, 1, 1, 1, 58, 58, 58, 58] 58
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])
total number of confs: 94
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040922 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040922
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040922/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040922
Building REAL300000040923
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040923'
/scratch/stefan/7769621/working/building/REAL300000040923 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040923

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040923/0 /scratch/stefan/7769621/working/building/REAL300000040923 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1051)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1051
`/scratch/stefan/7769621/working/3D/1051' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCC1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)O1)

`REAL300000040923.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040923.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040923/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040923 none O=C([O-])CCC1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 197, 194, 110, 110, 110, 110, 64, 64, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 110, 201, 201, 194, 194, 110, 110, 64, 10, 1, 1] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 630
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040923 none O=C([O-])CCC1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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]
0  hydrogens 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, 14, 8, 1, 1, 1, 1, 1, 1, 12, 12, 43, 110, 110, 110, 110, 110, 110, 110, 110, 1, 11, 11, 8, 8, 1, 1, 12, 43, 110, 110] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 21, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30, 31])
total number of confs: 257
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040923 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040923
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040923/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040923
Building REAL300000040924
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040924'
/scratch/stefan/7769621/working/building/REAL300000040924 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040924

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040924/0 /scratch/stefan/7769621/working/building/REAL300000040924 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1052)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1052
`/scratch/stefan/7769621/working/3D/1052' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NNC2=C3N=CN=C3N=C[N-]2)SC(Br)=C1)

`REAL300000040924.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040924.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040924/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040924 none O=C([O-])C1=C(C=NNC2=C3N=CN=C3N=C[N-]2)SC(Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 14, 1, 17, 1, 7, 6, 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]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [31, 30, 31, 30, 28, 28, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 28, 12, 1, 1, 30] 31
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 25])
total number of confs: 55
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040924 none O=C([O-])C1=C(C=NNC2=C3N=CN=C3N=C[N-]2)SC(Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 14, 1, 17, 1, 7, 6, 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]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 3, 3, 14, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 3, 14, 30, 30, 1] 31
rigid atoms, others: [1, 3, 4, 5, 17, 18, 19, 20, 25] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24])
total number of confs: 65
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040924 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040924
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040924/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040924
Building REAL300000040925
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040925'
/scratch/stefan/7769621/working/building/REAL300000040925 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040925

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040925/0 /scratch/stefan/7769621/working/building/REAL300000040925 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1053)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1053
`/scratch/stefan/7769621/working/3D/1053' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C2NC=C(C=NNC3=C4N=CN=C4NC=N3)C2=CC=C1)

`REAL300000040925.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040925.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040925/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040925 none O=C([O-])C1=C2NC=C(C=NNC3=C4N=CN=C4NC=N3)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 30, 30, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48, 30, 8, 1, 1, 1, 48, 48, 48] 48
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 33, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 79
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040925 none O=C([O-])C1=C2NC=C(C=NNC3=C4N=CN=C4NC=N3)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 10, 37, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 10, 36, 48, 48, 48, 1, 1, 1] 48
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 33, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30])
total number of confs: 109
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040925 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040925
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040925/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040925
Building REAL300000040926
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040926'
/scratch/stefan/7769621/working/building/REAL300000040926 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040926

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040926/0 /scratch/stefan/7769621/working/building/REAL300000040926 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1054)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1054
`/scratch/stefan/7769621/working/3D/1054' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=C2N=CN=C2NC=N1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1)

`REAL300000040926.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040926.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040926/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040926 none CC(=NNC1=C2N=CN=C2NC=N1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 5, 17, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 28, 28, 28, 1, 1, 1, 1, 1] 28
rigid atoms, others: [1, 34, 35, 36, 37, 33, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 26, 27, 28, 29, 30, 31])
total number of confs: 64
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040926 none CC(=NNC1=C2N=CN=C2NC=N1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [22, 22, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 22, 22, 22, 11, 1, 1, 1, 28, 28, 28, 28, 28] 28
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])
total number of confs: 54
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040926 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040926
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040926/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040926
Building REAL300000040927
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040927'
/scratch/stefan/7769621/working/building/REAL300000040927 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040927

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040927/0 /scratch/stefan/7769621/working/building/REAL300000040927 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1055)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1055
`/scratch/stefan/7769621/working/3D/1055' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC(C=NNC3=C4N=CN=C4NC=N3)=CC=C2O1)

`REAL300000040927.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040927.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040927/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040927 none O=C([O-])C1=CC2=CC(C=NNC3=C4N=CN=C4NC=N3)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 12, 7, 7, 7, 6, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [47, 47, 47, 47, 47, 47, 47, 28, 27, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 27, 8, 1, 1, 1, 47, 47] 47
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 79
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040927 none O=C([O-])C1=CC2=CC(C=NNC3=C4N=CN=C4NC=N3)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 12, 7, 7, 7, 6, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 35, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 12, 35, 47, 47, 47, 1, 1] 47
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30])
total number of confs: 109
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040927 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040927
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040927/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040927
Building REAL300000040928
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040928'
/scratch/stefan/7769621/working/building/REAL300000040928 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300000040928

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040928/0 /scratch/stefan/7769621/working/building/REAL300000040928 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1056)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1056
`/scratch/stefan/7769621/working/3D/1056' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2C(CN=NC3=C4N=CNC4=NC=N3)=CC=CN12)

`REAL300000040928.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040928.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040928/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040928 none O=C([O-])C1=CN=C2C(CN=NC3=C4N=CNC4=NC=N3)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [97, 97, 97, 97, 97, 97, 97, 40, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 97, 97, 97, 97, 97, 40, 40, 1, 1, 1, 97, 97, 97] 97
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 20, 21, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 210
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040928 none O=C([O-])C1=CN=C2C(CN=NC3=C4N=CNC4=NC=N3)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 56, 56, 97, 97, 97, 97, 97, 97, 97, 97, 1, 1, 1, 1, 1, 8, 8, 97, 97, 97, 1, 1, 1] 97
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 20, 21, 22, 23, 24, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29])
total number of confs: 148
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040928 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040928/1 /scratch/stefan/7769621/working/building/REAL300000040928 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 1057)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1057
`/scratch/stefan/7769621/working/3D/1057' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2C(C=NNC3=C4N=CNC4=NC=N3)=CC=CN12)

`REAL300000040928.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040928.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040928/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040928 none O=C([O-])C1=CN=C2C(C=NNC3=C4N=CNC4=NC=N3)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 8, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 20, 20, 20] 21
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 20, 21, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 31
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040928 none O=C([O-])C1=CN=C2C(C=NNC3=C4N=CNC4=NC=N3)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 8, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 3, 15, 20, 20, 20, 1, 1, 1] 21
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 20, 21, 22, 23, 24, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29])
total number of confs: 45
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040928 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `2'
/scratch/stefan/7769621/working/building/REAL300000040928/2 /scratch/stefan/7769621/working/building/REAL300000040928 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 2 (index: 1058)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1058
`/scratch/stefan/7769621/working/3D/1058' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2C(C=NNC3=C4NC=NC4=NC=N3)=CC=CN12)

`REAL300000040928.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300000040928.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040928/2/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`2.mol2' -> `2.mol2.original'
`output.mol2' -> `2.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040928 none O=C([O-])C1=CN=C2C(C=NNC3=C4NC=NC4=NC=N3)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 8, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 3, 7, 3, 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, 16, 16, 16, 16, 16, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 14, 4, 1, 1, 1, 16, 16, 16] 16
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 20, 21, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 25
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040928 none O=C([O-])C1=CN=C2C(C=NNC3=C4NC=NC4=NC=N3)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 1, 8, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
16  conformations in input
total number of sets (complete confs): 16
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 10, 16, 16, 16, 16, 1, 1, 1] 16
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 20, 21, 22, 23, 24, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29])
total number of confs: 37
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040928 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040928
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
2: /scratch/stefan/7769621/working/building/REAL300000040928/2.*
1: /scratch/stefan/7769621/working/building/REAL300000040928/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040928/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040928
Building REAL300000040929
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040929'
/scratch/stefan/7769621/working/building/REAL300000040929 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040929

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040929/0 /scratch/stefan/7769621/working/building/REAL300000040929 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1059)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1059
`/scratch/stefan/7769621/working/3D/1059' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(F)C=CC=C1C=NNC1=C2N=CN=C2NC=N1)

`REAL300000040929.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040929.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040929/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040929 none O=C([O-])C1=C(F)C=CC=C1C=NNC1=C2N=CN=C2NC=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 21, 21, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 21, 9, 1, 1, 1] 23
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26])
total number of confs: 40
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040929 none O=C([O-])C1=C(F)C=CC=C1C=NNC1=C2N=CN=C2NC=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 18, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 4, 18, 23, 23, 23] 23
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29])
total number of confs: 57
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040929 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040929
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040929/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040929
Building REAL300000040930
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040930'
/scratch/stefan/7769621/working/building/REAL300000040930 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040930

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040930/0 /scratch/stefan/7769621/working/building/REAL300000040930 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1060)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1060
`/scratch/stefan/7769621/working/3D/1060' -> `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=NNC2=C3N=CN=C3N=C[N-]2)O1)

`REAL300000040930.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040930.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040930/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040930 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=C3N=CN=C3N=C[N-]2)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'O.3', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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]
0  hydrogens need rotated
174  conformations in input
total number of sets (complete confs): 174
using faster count positions algorithm for large data
unique positions, atoms: [174, 174, 174, 174, 174, 174, 144, 63, 26, 26, 26, 26, 26, 26, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 174, 174, 174, 144, 144, 26, 26, 26, 26, 14, 5, 1, 1] 174
rigid atoms, others: [38, 39, 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])
total number of confs: 505
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040930 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=C3N=CN=C3N=C[N-]2)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'O.3', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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]
0  hydrogens need rotated
174  conformations in input
total number of sets (complete confs): 174
using faster count positions algorithm for large data
unique positions, atoms: [106, 106, 106, 106, 106, 106, 43, 10, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 26, 26, 26, 26, 26, 26, 26, 26, 106, 106, 106, 43, 43, 1, 1, 1, 1, 6, 21, 26, 26] 174
rigid atoms, others: [32, 33, 34, 35, 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, 36, 37, 38, 39])
total number of confs: 289
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040930 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=C3N=CN=C3N=C[N-]2)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'O.3', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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]
0  hydrogens need rotated
174  conformations in input
total number of sets (complete confs): 174
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 49, 106, 106, 106, 106, 106, 106, 136, 136, 172, 174, 174, 174, 174, 174, 174, 174, 174, 1, 1, 1, 9, 9, 106, 106, 106, 106, 136, 172, 174, 174] 174
rigid atoms, others: [1, 3, 4, 5, 6, 7, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 409
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040930 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040930/1 /scratch/stefan/7769621/working/building/REAL300000040930 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 1061)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1061
`/scratch/stefan/7769621/working/3D/1061' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(COC2=CC=CC=C2CN=NC2=C3N=CNC3=NC=N2)O1)

`REAL300000040930.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040930.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040930/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040930 none O=C([O-])C1=CC=C(COC2=CC=CC=C2CN=NC2=C3N=CNC3=NC=N2)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'O.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, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [101, 101, 101, 101, 101, 101, 95, 78, 61, 61, 61, 61, 61, 61, 32, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 101, 101, 101, 95, 95, 61, 61, 61, 61, 31, 32, 1, 1, 1] 101
rigid atoms, others: [38, 39, 40, 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])
total number of confs: 288
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040930 none O=C([O-])C1=CC=C(COC2=CC=CC=C2CN=NC2=C3N=CNC3=NC=N2)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'O.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, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [43, 43, 43, 43, 43, 43, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 33, 33, 61, 61, 61, 61, 61, 61, 61, 61, 43, 43, 43, 17, 17, 1, 1, 1, 1, 7, 7, 61, 61, 61] 101
rigid atoms, others: [32, 33, 34, 35, 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, 36, 37, 38, 39, 40])
total number of confs: 182
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040930 none O=C([O-])C1=CC=C(COC2=CC=CC=C2CN=NC2=C3N=CNC3=NC=N2)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'O.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, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 30, 43, 43, 30, 43, 43, 43, 51, 87, 87, 101, 101, 101, 101, 101, 101, 101, 101, 1, 1, 1, 8, 8, 43, 43, 30, 43, 51, 51, 101, 101, 101] 101
rigid atoms, others: [1, 3, 4, 5, 6, 7, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 237
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040930 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040930
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040930/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040930/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040930
Building REAL300000040931
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040931'
/scratch/stefan/7769621/working/building/REAL300000040931 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040931

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040931/0 /scratch/stefan/7769621/working/building/REAL300000040931 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1062)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1062
`/scratch/stefan/7769621/working/3D/1062' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Br)C=CC=C1C=NNC1=C2N=CN=C2N=C[N-]1)

`REAL300000040931.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040931.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040931/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040931 none O=C([O-])C1=C(Br)C=CC=C1C=NNC1=C2N=CN=C2N=C[N-]1 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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 11, 1, 1] 15
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040931 none O=C([O-])C1=C(Br)C=CC=C1C=NNC1=C2N=CN=C2N=C[N-]1 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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 3, 3, 7, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 3, 7, 15, 15] 15
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28])
total number of confs: 33
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040931 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040931
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040931/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040931
Building REAL300000040932
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040932'
/scratch/stefan/7769621/working/building/REAL300000040932 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040932

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040932/0 /scratch/stefan/7769621/working/building/REAL300000040932 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1063)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1063
`/scratch/stefan/7769621/working/3D/1063' -> `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=NNC1=C2N=CN=C2NC=N1)

`REAL300000040932.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040932.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040932/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040932 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NNC1=C2N=CN=C2NC=N1 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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 68, 68, 68, 68, 68, 79, 68, 68, 68, 68, 68, 68, 72, 72, 34, 34, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 68, 79, 79, 79, 68, 68, 34, 10, 1, 1, 1] 83
rigid atoms, others: [39, 40, 41, 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])
total number of confs: 168
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040932 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NNC1=C2N=CN=C2NC=N1 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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 8, 8, 35, 68, 68, 68, 68, 68, 68, 68, 68, 3, 3, 3, 1, 3, 3, 3, 1, 1, 8, 35, 68, 68, 68] 83
rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 15, 16, 35, 36, 31] set([0, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 37, 38, 39, 40, 41])
total number of confs: 144
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040932 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040932
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040932/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040932
Building REAL300000040933
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040933'
/scratch/stefan/7769621/working/building/REAL300000040933 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040933

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040933/0 /scratch/stefan/7769621/working/building/REAL300000040933 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1064)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1064
`/scratch/stefan/7769621/working/3D/1064' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2OCOC2=C1C=NNC1=C2N=CN=C2NC=N1)

`REAL300000040933.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040933.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040933/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040933 none O=C([O-])C1=CC=C2OCOC2=C1C=NNC1=C2N=CN=C2NC=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 26, 26, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 26, 10, 1, 1, 1] 38
rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29])
total number of confs: 64
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040933 none O=C([O-])C1=CC=C2OCOC2=C1C=NNC1=C2N=CN=C2NC=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 25, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 6, 25, 38, 38, 38] 38
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27] set([0, 32, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31])
total number of confs: 88
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040933 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040933
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040933/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040933
Building REAL300000040934
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040934'
/scratch/stefan/7769621/working/building/REAL300000040934 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040934

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040934/0 /scratch/stefan/7769621/working/building/REAL300000040934 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1065)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1065
`/scratch/stefan/7769621/working/3D/1065' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=CC=C(C(=O)[O-])C(C=NNC2=C3N=CN=C3NC=N2)=C1)

`REAL300000040934.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040934.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040934/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040934 none N#CC1=CC=C(C(=O)[O-])C(C=NNC2=C3N=CN=C3NC=N2)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 27, 21, 21, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 21, 9, 1, 1, 1, 27] 27
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 30])
total number of confs: 47
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040934 none N#CC1=CC=C(C(=O)[O-])C(C=NNC2=C3N=CN=C3NC=N2)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 6, 6, 20, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 6, 20, 27, 27, 27, 1] 27
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 22, 23, 24, 30] set([7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29])
total number of confs: 65
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040934 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040934
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040934/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040934
Building REAL300000040935
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040935'
/scratch/stefan/7769621/working/building/REAL300000040935 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040935

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040935/0 /scratch/stefan/7769621/working/building/REAL300000040935 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1066)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1066
`/scratch/stefan/7769621/working/3D/1066' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)C=C1Cl)

`REAL300000040935.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040935.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040935/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040935 none O=C([O-])COC1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)C=C1Cl 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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 8, 1, 8, 1, 8, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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]
0  hydrogens need rotated
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, 167, 79, 79, 79, 79, 32, 32, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 201, 201, 79, 79, 32, 6, 1, 1, 79] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 449
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040935 none O=C([O-])COC1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)C=C1Cl 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.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 8, 1, 8, 1, 8, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 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]
0  hydrogens 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, 26, 54, 7, 1, 1, 1, 1, 1, 1, 6, 6, 41, 79, 79, 79, 79, 79, 79, 79, 79, 1, 1, 1, 26, 26, 1, 1, 6, 41, 79, 79, 1] 201
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 21, 22, 23, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 28, 29, 30, 31])
total number of confs: 325
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040935 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040935
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040935/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040935
Building REAL300000040936
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040936'
/scratch/stefan/7769621/working/building/REAL300000040936 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040936

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040936/0 /scratch/stefan/7769621/working/building/REAL300000040936 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1067)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1067
`/scratch/stefan/7769621/working/3D/1067' -> `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=NNC2=C3N=CN=C3N=C[N-]2)C=C1)

`REAL300000040936.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040936.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040936/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040936 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 84, 84, 82, 45, 20, 45, 45, 20, 45, 45, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 84, 84, 82, 45, 45, 20, 6, 1, 1, 45, 45] 84
rigid atoms, others: [33, 34, 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, 35, 36])
total number of confs: 394
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040936 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC2=C3N=CN=C3N=C[N-]2)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', '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, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 7, 7, 31, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 9, 9, 5, 1, 1, 7, 31, 45, 45, 1, 1] 84
rigid atoms, others: [35, 36, 5, 8, 9, 10, 11, 12, 24, 25, 29, 30] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34])
total number of confs: 137
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040936 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040936
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040936/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040936
Building REAL300000040937
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040937'
/scratch/stefan/7769621/working/building/REAL300000040937 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300000040937

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040937/0 /scratch/stefan/7769621/working/building/REAL300000040937 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1068)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1068
`/scratch/stefan/7769621/working/3D/1068' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NSC(C=NNC2=C3N=CNC3=NC=N2)=C1C(=O)[O-])

`REAL300000040937.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040937.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040937/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040937 none CC1=NSC(C=NNC2=C3N=CNC3=NC=N2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [33, 33, 33, 33, 28, 28, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 28, 8, 1, 1, 1] 33
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25])
total number of confs: 53
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040937 none CC1=NSC(C=NNC2=C3N=CNC3=NC=N2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 18, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 3, 3, 2, 2, 2, 4, 18, 33, 33, 33] 33
rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 79
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040937 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040937/1 /scratch/stefan/7769621/working/building/REAL300000040937 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 1069)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1069
`/scratch/stefan/7769621/working/3D/1069' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NSC(CN=NC2=C3N=CNC3=NC=N2)=C1C(=O)[O-])

`REAL300000040937.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040937.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040937/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040937 none CC1=NSC(CN=NC2=C3N=CNC3=NC=N2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
111  conformations in input
total number of sets (complete confs): 111
using faster count positions algorithm for large data
unique positions, atoms: [111, 111, 111, 111, 40, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 111, 111, 111, 40, 40, 1, 1, 1] 111
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25])
total number of confs: 226
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040937 none CC1=NSC(CN=NC2=C3N=CNC3=NC=N2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 6, 46, 46, 111, 111, 111, 111, 111, 111, 111, 111, 1, 1, 3, 3, 2, 2, 2, 6, 6, 111, 111, 111] 111
rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 178
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040937 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `2'
/scratch/stefan/7769621/working/building/REAL300000040937/2 /scratch/stefan/7769621/working/building/REAL300000040937 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 2 (index: 1070)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1070
`/scratch/stefan/7769621/working/3D/1070' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NSC(C=NNC2=C3NC=NC3=NC=N2)=C1C(=O)[O-])

`REAL300000040937.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300000040937.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040937/2/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`2.mol2' -> `2.mol2.original'
`output.mol2' -> `2.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040937 none CC1=NSC(C=NNC2=C3NC=NC3=NC=N2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 2, 2, 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, 16, 16, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 12, 4, 1, 1, 1] 16
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25])
total number of confs: 27
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040937 none CC1=NSC(C=NNC2=C3NC=NC3=NC=N2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
16  conformations in input
total number of sets (complete confs): 16
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 14, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 3, 3, 2, 2, 2, 9, 14, 16, 16, 16] 16
rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 49
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040937 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040937
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
2: /scratch/stefan/7769621/working/building/REAL300000040937/2.*
1: /scratch/stefan/7769621/working/building/REAL300000040937/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040937/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040937
Building REAL300000040938
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040938'
/scratch/stefan/7769621/working/building/REAL300000040938 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300000040938

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040938/0 /scratch/stefan/7769621/working/building/REAL300000040938 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1071)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1071
`/scratch/stefan/7769621/working/3D/1071' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=C(C=NNC3=C4N=CNC4=NC=N3)C(F)=CC=C2S1)

`REAL300000040938.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040938.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040938/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040938 none O=C([O-])C1=CC2=C(C=NNC3=C4N=CNC4=NC=N3)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', 'N.pl3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [48, 47, 48, 47, 47, 47, 32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47, 32, 8, 1, 1, 1, 47, 47] 48
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: 72
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040938 none O=C([O-])C1=CC2=C(C=NNC3=C4N=CNC4=NC=N3)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', 'N.pl3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 11, 11, 40, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 11, 40, 47, 47, 47, 1, 1] 48
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30])
total number of confs: 117
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040938 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040938/1 /scratch/stefan/7769621/working/building/REAL300000040938 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 1072)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1072
`/scratch/stefan/7769621/working/3D/1072' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=C(CN=NC3=C4N=CNC4=NC=N3)C(F)=CC=C2S1)

`REAL300000040938.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040938.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040938/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040938 none O=C([O-])C1=CC2=C(CN=NC3=C4N=CNC4=NC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 15, 1, 1, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [95, 95, 95, 95, 95, 95, 46, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 94, 95, 95, 95, 46, 46, 1, 1, 1, 95, 94] 95
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: 215
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040938 none O=C([O-])C1=CC2=C(CN=NC3=C4N=CNC4=NC=N3)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 15, 1, 1, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 54, 54, 95, 95, 95, 95, 95, 95, 95, 95, 1, 1, 1, 1, 1, 1, 1, 8, 8, 95, 95, 95, 1, 1] 95
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30])
total number of confs: 152
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040938 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `2'
/scratch/stefan/7769621/working/building/REAL300000040938/2 /scratch/stefan/7769621/working/building/REAL300000040938 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 2 (index: 1073)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1073
`/scratch/stefan/7769621/working/3D/1073' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=C(C=NNC3=C4NC=NC4=NC=N3)C(F)=CC=C2S1)

`REAL300000040938.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300000040938.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040938/2/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`2.mol2' -> `2.mol2.original'
`output.mol2' -> `2.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040938 none O=C([O-])C1=CC2=C(C=NNC3=C4NC=NC4=NC=N3)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', 'N.pl3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 15, 1, 1, 1, 14, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 14, 14, 14, 14, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 8, 6, 1, 1, 1, 14, 14] 14
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: 25
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040938 none O=C([O-])C1=CC2=C(C=NNC3=C4NC=NC4=NC=N3)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', 'N.pl3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 1, 15, 1, 1, 1, 14, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 3, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 11, 11, 13, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 11, 13, 14, 14, 14, 1, 1] 14
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30])
total number of confs: 37
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040938 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040938
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
2: /scratch/stefan/7769621/working/building/REAL300000040938/2.*
1: /scratch/stefan/7769621/working/building/REAL300000040938/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040938/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040938
Building REAL300000040939
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040939'
/scratch/stefan/7769621/working/building/REAL300000040939 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040939

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040939/0 /scratch/stefan/7769621/working/building/REAL300000040939 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1074)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1074
`/scratch/stefan/7769621/working/3D/1074' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=NNC1=C2N=CN=C2NC=N1)

`REAL300000040939.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040939.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040939/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040939 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=C2N=CN=C2NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 22, 22, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 22, 8, 1, 1, 1] 39
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: 60
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040939 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=C2N=CN=C2NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 24, 39, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 1, 1, 1, 10, 24, 39, 39, 39] 39
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31])
total number of confs: 84
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040939 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040939
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040939/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040939
Building REAL300000040940
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040940'
/scratch/stefan/7769621/working/building/REAL300000040940 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040940

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040940/0 /scratch/stefan/7769621/working/building/REAL300000040940 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1075)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1075
`/scratch/stefan/7769621/working/3D/1075' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=C4N=CN=C4N=C[N-]3)=N2)C1)

`REAL300000040940.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040940.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040940/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040940 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=C4N=CN=C4N=C[N-]3)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 72, 201, 72, 72, 72, 54, 54, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 72, 201, 201, 201, 72, 72, 54, 8, 1, 1, 201, 201] 201
rigid atoms, others: [32, 33, 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, 34, 35])
total number of confs: 454
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040940 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=C4N=CN=C4N=C[N-]3)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 13, 25, 13, 13, 13, 1, 13, 1, 1, 1, 1, 1, 4, 4, 23, 72, 72, 72, 72, 72, 72, 72, 72, 1, 13, 13, 13, 1, 1, 4, 23, 72, 72, 13, 13] 201
rigid atoms, others: [6, 8, 9, 10, 11, 12, 24, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35])
total number of confs: 194
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040940 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=C4N=CN=C4N=C[N-]3)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 8, 1, 8, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 27, 27, 107, 201, 201, 201, 201, 201, 201, 201, 201, 13, 1, 1, 1, 13, 13, 27, 107, 201, 201, 1, 1] 201
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 35, 25, 26, 27] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33])
total number of confs: 409
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040940 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040940
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040940/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040940
Building REAL300000040941
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040941'
/scratch/stefan/7769621/working/building/REAL300000040941 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040941

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040941/0 /scratch/stefan/7769621/working/building/REAL300000040941 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1076)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1076
`/scratch/stefan/7769621/working/3D/1076' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NCC2=CC=CC=C2OCC(=O)[O-])O1)

`REAL300000040941.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040941.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040941/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040941 none CC1=NC(C#N)=C(N=NCC2=CC=CC=C2OCC(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 12, 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, 3, 7, 7, 2, 2, 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: [46, 46, 46, 46, 46, 46, 40, 40, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 27, 54, 54, 46, 46, 46, 46, 8, 8, 1, 1, 1, 1, 27, 27] 201
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 245
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040941 none CC1=NC(C#N)=C(N=NCC2=CC=CC=C2OCC(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 12, 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, 3, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 14, 46, 46, 21, 46, 46, 46, 115, 201, 201, 201, 1, 2, 2, 2, 14, 14, 46, 46, 45, 46, 201, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 711
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040941 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040941
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040941/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040941
Building REAL300000040942
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040942'
/scratch/stefan/7769621/working/building/REAL300000040942 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040942

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040942/0 /scratch/stefan/7769621/working/building/REAL300000040942 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1077)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1077
`/scratch/stefan/7769621/working/3D/1077' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NC(C)C2=CC=C(C3=CC=C(C(=O)[O-])O3)C=C2)O1)

`REAL300000040942.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040942.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040942/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040942 none CC1=NC(C#N)=C(N=NC(C)C2=CC=C(C3=CC=C(C(=O)[O-])O3)C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 125, 125, 14, 1, 13, 1, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 201, 201, 201, 201, 13, 14, 14, 13, 12, 12, 1, 1, 12, 12] 201
rigid atoms, others: [35, 36, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38])
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: REAL300000040942 none CC1=NC(C#N)=C(N=NC(C)C2=CC=C(C3=CC=C(C(=O)[O-])O3)C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 12, 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, 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: [93, 93, 93, 93, 93, 93, 44, 44, 7, 1, 7, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 93, 93, 93, 93, 7, 7, 7, 7, 1, 1, 12, 12, 1, 1] 201
rigid atoms, others: [33, 34, 37, 38, 9, 11, 12, 13, 14, 15, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 151
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040942 none CC1=NC(C#N)=C(N=NC(C)C2=CC=C(C3=CC=C(C(=O)[O-])O3)C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 12, 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, 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, 1, 1, 1, 8, 8, 43, 43, 93, 93, 47, 56, 201, 201, 201, 201, 201, 201, 201, 93, 93, 1, 2, 2, 2, 43, 43, 43, 43, 93, 93, 201, 201, 93, 93] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 520
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040942 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040942
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040942/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040942
Building REAL300000040943
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040943'
/scratch/stefan/7769621/working/building/REAL300000040943 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040943

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040943/0 /scratch/stefan/7769621/working/building/REAL300000040943 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1078)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1078
`/scratch/stefan/7769621/working/3D/1078' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(CN=NC2=C(C#N)N=C(C)O2)=CC=C1OCC(=O)[O-])

`REAL300000040943.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040943.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040943/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040943 none COC1=CC(CN=NC2=C(C#N)N=C(C)O2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.1', 'N.1', 'N.2', 'C.2', 'C.3', 'O.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']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 1, 12, 5, 1, 11, 11, 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, 3, 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: [79, 41, 41, 41, 10, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 109, 197, 201, 201, 79, 79, 79, 41, 10, 9, 2, 2, 2, 41, 41, 197, 197] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 714
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040943 none COC1=CC(CN=NC2=C(C#N)N=C(C)O2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.1', 'N.1', 'N.2', 'C.2', 'C.3', 'O.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']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 1, 12, 5, 1, 11, 11, 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, 3, 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, 6, 40, 40, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 9, 19, 28, 28, 3, 3, 3, 1, 6, 6, 41, 41, 41, 1, 1, 19, 19] 201
rigid atoms, others: [1, 2, 3, 4, 5, 33, 34, 16, 17, 18, 19, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 153
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040943 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040943
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040943/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040943
Building REAL300000040944
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040944'
/scratch/stefan/7769621/working/building/REAL300000040944 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040944

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040944/0 /scratch/stefan/7769621/working/building/REAL300000040944 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1079)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1079
`/scratch/stefan/7769621/working/3D/1079' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NCC2=CC=C(OCC(=O)[O-])C=C2)O1)

`REAL300000040944.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040944.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040944/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040944 none CC1=NC(C#N)=C(N=NCC2=CC=C(OCC(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 12, 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, 3, 7, 7, 2, 2, 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: [38, 38, 38, 38, 38, 38, 30, 30, 4, 1, 1, 1, 1, 1, 1, 6, 22, 34, 34, 1, 1, 38, 39, 39, 39, 4, 4, 1, 1, 22, 22, 1, 1] 201
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])
total number of confs: 169
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040944 none CC1=NC(C#N)=C(N=NCC2=CC=C(OCC(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 12, 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, 3, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 38, 38, 15, 26, 116, 201, 201, 201, 38, 38, 1, 2, 2, 2, 15, 15, 38, 38, 201, 201, 38, 38] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 724
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040944 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040944
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040944/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040944
Building REAL300000040945
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040945'
/scratch/stefan/7769621/working/building/REAL300000040945 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040945

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040945/0 /scratch/stefan/7769621/working/building/REAL300000040945 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1080)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1080
`/scratch/stefan/7769621/working/3D/1080' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NC(C)C2=CC=CC(OCC(=O)[O-])=C2)O1)

`REAL300000040945.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040945.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040945/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040945 none CC1=NC(C#N)=C(N=NC(C)C2=CC=CC(OCC(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 12, 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, 3, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [41, 41, 41, 41, 41, 41, 33, 33, 7, 1, 7, 1, 1, 1, 1, 1, 1, 7, 21, 32, 32, 1, 41, 41, 41, 41, 7, 7, 7, 7, 1, 1, 1, 21, 21, 1] 201
rigid atoms, others: [32, 35, 9, 11, 12, 13, 14, 15, 16, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 166
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040945 none CC1=NC(C#N)=C(N=NC(C)C2=CC=CC(OCC(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 12, 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, 3, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 15, 41, 41, 41, 41, 41, 130, 201, 201, 201, 41, 1, 2, 2, 2, 15, 15, 15, 15, 41, 41, 41, 201, 201, 41] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 588
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040945 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040945
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040945/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040945
Building REAL300000040946
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040946'
/scratch/stefan/7769621/working/building/REAL300000040946 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040946

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040946/0 /scratch/stefan/7769621/working/building/REAL300000040946 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1081)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1081
`/scratch/stefan/7769621/working/3D/1081' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NC(C)C2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)O1)

`REAL300000040946.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040946.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040946/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040946 none CC1=NC(C#N)=C(N=NC(C)C2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 12, 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, 6, 6, 4, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [57, 57, 57, 57, 57, 57, 25, 25, 5, 1, 5, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 19, 19, 1, 1, 57, 57, 57, 57, 5, 5, 5, 5, 1, 1, 9, 17, 17, 1, 1] 188
rigid atoms, others: [33, 34, 38, 39, 9, 11, 12, 13, 14, 15, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37])
total number of confs: 162
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040946 none CC1=NC(C#N)=C(N=NC(C)C2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 12, 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, 6, 6, 4, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 30, 30, 57, 57, 30, 30, 95, 95, 95, 164, 188, 188, 188, 57, 57, 1, 2, 2, 2, 30, 30, 30, 30, 57, 57, 164, 188, 188, 57, 57] 188
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 891
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040946 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040946
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040946/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040946
Building REAL300000040947
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040947'
/scratch/stefan/7769621/working/building/REAL300000040947 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040947

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040947/0 /scratch/stefan/7769621/working/building/REAL300000040947 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1082)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1082
`/scratch/stefan/7769621/working/3D/1082' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NC(C)C2=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C2)O1)

`REAL300000040947.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040947.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040947/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040947 none CC1=NC(C#N)=C(N=NC(C)C2=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [28, 28, 28, 28, 28, 28, 21, 21, 5, 1, 5, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 1, 1, 28, 28, 28, 28, 5, 5, 5, 5, 1, 1, 9, 9, 9, 9, 9, 1, 1] 90
rigid atoms, others: [34, 35, 9, 42, 11, 12, 13, 14, 15, 41, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40])
total number of confs: 72
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040947 none CC1=NC(C#N)=C(N=NC(C)C2=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 28, 28, 17, 17, 48, 48, 48, 90, 90, 90, 90, 90, 28, 28, 1, 2, 2, 2, 17, 17, 17, 17, 28, 28, 90, 90, 90, 90, 90, 28, 28] 90
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 26] set([8, 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])
total number of confs: 373
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040947 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040947
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040947/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040947
Building REAL300000040948
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040948'
/scratch/stefan/7769621/working/building/REAL300000040948 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040948

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040948/0 /scratch/stefan/7769621/working/building/REAL300000040948 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1083)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1083
`/scratch/stefan/7769621/working/3D/1083' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NC(C)C2=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C2)O1)

`REAL300000040948.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040948.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040948/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040948 none CC1=NC(C#N)=C(N=NC(C)C2=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 7, 5, 1, 11, 11, 1, 1, 12, 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, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 1, 1, 6, 6, 6, 6, 3, 3, 3, 3, 1, 1, 5, 5, 5, 5, 1, 1] 15
rigid atoms, others: [35, 36, 9, 42, 11, 12, 13, 14, 15, 41, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40])
total number of confs: 31
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040948 none CC1=NC(C#N)=C(N=NC(C)C2=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 7, 5, 1, 11, 11, 1, 1, 12, 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, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 4, 4, 9, 9, 9, 15, 15, 15, 15, 15, 15, 6, 6, 1, 2, 2, 2, 4, 4, 4, 4, 6, 6, 15, 15, 15, 15, 6, 6] 15
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 27] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 74
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040948 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040948
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040948/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040948
Building REAL300000040949
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040949'
/scratch/stefan/7769621/working/building/REAL300000040949 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040949

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040949/0 /scratch/stefan/7769621/working/building/REAL300000040949 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1084)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1084
`/scratch/stefan/7769621/working/3D/1084' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NCC2=CC=C(OCCC(=O)[O-])C=C2)O1)

`REAL300000040949.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040949.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040949/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040949 none CC1=NC(C#N)=C(N=NCC2=CC=C(OCCC(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 12, 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, 3, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [50, 50, 50, 50, 50, 50, 32, 32, 4, 1, 1, 1, 1, 1, 1, 6, 18, 19, 29, 27, 1, 1, 50, 51, 51, 51, 4, 4, 1, 1, 18, 18, 18, 18, 1, 1] 201
rigid atoms, others: [34, 35, 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])
total number of confs: 179
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040949 none CC1=NC(C#N)=C(N=NCC2=CC=C(OCCC(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 12, 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, 3, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 23, 50, 50, 23, 36, 171, 200, 201, 201, 199, 50, 50, 1, 2, 2, 2, 23, 23, 50, 50, 200, 201, 200, 200, 50, 50] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 522
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040949 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040949
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040949/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040949
Building REAL300000040950
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040950'
/scratch/stefan/7769621/working/building/REAL300000040950 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040950

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040950/0 /scratch/stefan/7769621/working/building/REAL300000040950 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1085)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1085
`/scratch/stefan/7769621/working/3D/1085' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NCC2=CC(Br)=CC=C2OCC(=O)[O-])O1)

`REAL300000040950.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040950.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040950/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040950 none CC1=NC(C#N)=C(N=NCC2=CC(Br)=CC=C2OCC(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 12, 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, 3, 7, 7, 2, 2, 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: [47, 47, 47, 47, 47, 47, 43, 42, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 28, 52, 52, 47, 47, 47, 47, 7, 7, 1, 1, 1, 28, 28] 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, 32, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 247
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040950 none CC1=NC(C#N)=C(N=NCC2=CC(Br)=CC=C2OCC(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 12, 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, 3, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 12, 47, 47, 47, 12, 47, 47, 47, 105, 201, 201, 201, 1, 2, 2, 2, 12, 12, 47, 46, 47, 201, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 766
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040950 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040950
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040950/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040950
Building REAL300000040951
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040951'
/scratch/stefan/7769621/working/building/REAL300000040951 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040951

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040951/0 /scratch/stefan/7769621/working/building/REAL300000040951 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1086)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1086
`/scratch/stefan/7769621/working/3D/1086' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NCC2=CC=CC(OC(C)C(=O)[O-])=C2)O1)

`REAL300000040951.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040951.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040951/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040951 none CC1=NC(C#N)=C(N=NCC2=CC=CC(OC(C)C(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 12, 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, 3, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [49, 49, 49, 49, 49, 49, 47, 47, 8, 1, 1, 1, 1, 1, 1, 1, 8, 19, 19, 24, 24, 1, 49, 49, 49, 49, 8, 8, 1, 1, 1, 19, 19, 19, 19, 1] 201
rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 15, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 155
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040951 none CC1=NC(C#N)=C(N=NCC2=CC=CC(OC(C)C(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 12, 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, 3, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 49, 49, 49, 49, 49, 158, 201, 201, 201, 201, 49, 1, 2, 2, 2, 10, 11, 49, 49, 49, 201, 201, 201, 201, 49] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 461
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040951 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040951
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040951/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040951
Building REAL300000040952
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040952'
/scratch/stefan/7769621/working/building/REAL300000040952 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040952

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040952/0 /scratch/stefan/7769621/working/building/REAL300000040952 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1087)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1087
`/scratch/stefan/7769621/working/3D/1087' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NCC2=CC=CC(OCCC(=O)[O-])=C2)O1)

`REAL300000040952.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040952.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040952/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040952 none CC1=NC(C#N)=C(N=NCC2=CC=CC(OCCC(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 12, 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, 3, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 48, 48, 48, 48, 47, 47, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 14, 14, 1, 48, 48, 48, 48, 7, 7, 1, 1, 1, 7, 7, 7, 7, 1] 201
rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 15, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 104
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040952 none CC1=NC(C#N)=C(N=NCC2=CC=CC(OCCC(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 12, 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, 3, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 10, 48, 48, 48, 48, 48, 201, 201, 201, 201, 201, 48, 1, 2, 2, 2, 9, 10, 48, 48, 48, 201, 201, 201, 201, 48] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 279
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040952 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040952
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040952/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040952
Building REAL300000040953
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040953'
/scratch/stefan/7769621/working/building/REAL300000040953 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040953

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040953/0 /scratch/stefan/7769621/working/building/REAL300000040953 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1088)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1088
`/scratch/stefan/7769621/working/3D/1088' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NCC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)O1)

`REAL300000040953.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040953.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040953/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040953 none CC1=NC(C#N)=C(N=NCC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 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, 3, 7, 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]
0  hydrogens need rotated
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, 179, 179, 43, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 201, 201, 201, 201, 43, 43, 3, 7, 7, 3, 3, 1, 1, 1, 1, 7] 201
rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42])
total number of confs: 371
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: REAL300000040953 none CC1=NC(C#N)=C(N=NCC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 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, 3, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [85, 85, 85, 85, 85, 85, 64, 64, 8, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 7, 9, 9, 1, 85, 85, 85, 85, 8, 8, 1, 1, 1, 3, 3, 7, 7, 7, 7, 1] 201
rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41])
total number of confs: 148
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040953 none CC1=NC(C#N)=C(N=NCC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 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, 3, 7, 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]
0  hydrogens need rotated
201  conformations 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, 3, 3, 19, 85, 85, 85, 85, 85, 141, 141, 201, 201, 201, 201, 201, 201, 201, 201, 85, 1, 2, 2, 2, 18, 19, 85, 85, 85, 141, 141, 201, 201, 201, 201, 85] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 358
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040953 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040953
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040953/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040953
Building REAL300000040954
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040954'
/scratch/stefan/7769621/working/building/REAL300000040954 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040954

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040954/0 /scratch/stefan/7769621/working/building/REAL300000040954 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1089)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1089
`/scratch/stefan/7769621/working/3D/1089' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NCC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)O1)

`REAL300000040954.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040954.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040954/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040954 none CC1=NC(C#N)=C(N=NCC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 1, 12, 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, 3, 7, 7, 2, 2, 7, 7, 3, 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: [57, 57, 57, 57, 57, 57, 55, 55, 9, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 1, 1, 2, 2, 1, 57, 57, 57, 57, 9, 9, 1, 1, 17, 17, 1] 201
rigid atoms, others: [34, 9, 10, 11, 12, 13, 14, 19, 20, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 24, 25, 26, 27, 28, 29, 32, 33])
total number of confs: 139
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040954 none CC1=NC(C#N)=C(N=NCC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 1, 12, 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, 3, 7, 7, 2, 2, 7, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 57, 57, 12, 14, 182, 201, 201, 201, 57, 57, 57, 57, 57, 1, 2, 2, 2, 12, 11, 57, 57, 201, 201, 57] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 452
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040954 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040954
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040954/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040954
Building REAL300000040955
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040955'
/scratch/stefan/7769621/working/building/REAL300000040955 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040955

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040955/0 /scratch/stefan/7769621/working/building/REAL300000040955 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1090)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1090
`/scratch/stefan/7769621/working/3D/1090' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])OC(COC2=CC=C(CN=NC3=C(C#N)N=C(C)O3)C=C2)=C1)

`REAL300000040955.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040955.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040955/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040955 none CC1=C(C(=O)[O-])OC(COC2=CC=C(CN=NC3=C(C#N)N=C(C)O3)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.3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.1', 'N.1', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 1, 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, 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, 201, 52, 52, 31, 11, 52, 52, 11, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 201, 201, 201, 201, 52, 53, 52, 52, 11, 11, 2, 2, 2, 52, 52, 201] 201
rigid atoms, others: [16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 408
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: REAL300000040955 none CC1=C(C(=O)[O-])OC(COC2=CC=C(CN=NC3=C(C#N)N=C(C)O3)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.3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.1', 'N.1', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 1, 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, 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: [6, 6, 6, 6, 11, 11, 6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 50, 50, 52, 52, 52, 52, 52, 52, 52, 1, 1, 6, 6, 6, 6, 1, 1, 1, 1, 8, 8, 53, 53, 53, 1, 1, 6] 201
rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 40, 41, 25, 26, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 35, 36, 37, 38, 39, 42])
total number of confs: 111
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040955 none CC1=C(C(=O)[O-])OC(COC2=CC=C(CN=NC3=C(C#N)N=C(C)O3)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.3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.1', 'N.1', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 33, 198, 198, 201, 201, 201, 201, 201, 201, 201, 6, 6, 1, 2, 2, 2, 6, 6, 6, 6, 33, 33, 201, 201, 201, 5, 6, 1] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 42, 27] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 329
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040955 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040955
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040955/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040955
Building REAL300000040956
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040956'
/scratch/stefan/7769621/working/building/REAL300000040956 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040956

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040956/0 /scratch/stefan/7769621/working/building/REAL300000040956 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1091)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1091
`/scratch/stefan/7769621/working/3D/1091' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NCC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)O1)

`REAL300000040956.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040956.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040956/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040956 none CC1=NC(C#N)=C(N=NCC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 64, 11, 10, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 10, 201, 201, 201, 201, 64, 64, 10, 11, 11, 5, 5, 1, 1, 1, 1, 11] 201
rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42])
total number of confs: 419
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: REAL300000040956 none CC1=NC(C#N)=C(N=NCC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [44, 44, 44, 44, 44, 44, 43, 43, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 10, 10, 10, 10, 11, 11, 11, 10, 1, 44, 44, 44, 44, 7, 7, 1, 1, 1, 2, 2, 11, 11, 10, 11, 1] 201
rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41])
total number of confs: 87
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040956 none CC1=NC(C#N)=C(N=NCC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 2, 2, 10, 44, 44, 44, 44, 44, 70, 70, 201, 201, 201, 201, 201, 201, 201, 201, 44, 1, 2, 2, 2, 9, 10, 44, 44, 44, 70, 70, 201, 201, 201, 201, 44] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 316
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040956 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040956
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040956/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040956
Building REAL300000040957
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040957'
/scratch/stefan/7769621/working/building/REAL300000040957 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040957

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040957/0 /scratch/stefan/7769621/working/building/REAL300000040957 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1092)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1092
`/scratch/stefan/7769621/working/3D/1092' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NCC2=CC=CC(OCC(=O)[O-])=C2)O1)

`REAL300000040957.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040957.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040957/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040957 none CC1=NC(C#N)=C(N=NCC2=CC=CC(OCC(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 12, 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, 3, 7, 7, 2, 2, 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: [43, 43, 43, 43, 43, 43, 42, 42, 8, 1, 1, 1, 1, 1, 1, 1, 7, 17, 26, 26, 1, 43, 43, 43, 43, 8, 8, 1, 1, 1, 17, 17, 1] 201
rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 146
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040957 none CC1=NC(C#N)=C(N=NCC2=CC=CC(OCC(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 12, 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, 3, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 10, 43, 43, 43, 43, 43, 148, 201, 201, 201, 43, 1, 2, 2, 2, 9, 10, 43, 43, 43, 201, 201, 43] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 531
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040957 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040957
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040957/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040957
Building REAL300000040958
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040958'
/scratch/stefan/7769621/working/building/REAL300000040958 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040958

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040958/0 /scratch/stefan/7769621/working/building/REAL300000040958 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1093)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1093
`/scratch/stefan/7769621/working/3D/1093' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NCC2=CC=C(OCC3=C(C(=O)[O-])C=CO3)C=C2)O1)

`REAL300000040958.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040958.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040958/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040958 none CC1=NC(C#N)=C(N=NCC2=CC=C(OCC3=C(C(=O)[O-])C=CO3)C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 12, 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, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 164, 164, 45, 15, 15, 15, 15, 8, 6, 1, 1, 1, 1, 2, 2, 1, 1, 1, 15, 15, 201, 201, 201, 201, 45, 45, 14, 15, 6, 6, 1, 1, 15, 15] 201
rigid atoms, others: [36, 37, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39])
total number of confs: 403
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040958 none CC1=NC(C#N)=C(N=NCC2=CC=C(OCC3=C(C(=O)[O-])C=CO3)C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 12, 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, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [69, 69, 69, 69, 69, 69, 35, 35, 4, 1, 1, 1, 1, 1, 1, 2, 6, 15, 15, 15, 15, 15, 15, 15, 1, 1, 69, 70, 70, 70, 4, 4, 1, 1, 6, 6, 15, 15, 1, 1] 201
rigid atoms, others: [32, 33, 38, 39, 9, 10, 11, 12, 13, 14, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37])
total number of confs: 146
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040958 none CC1=NC(C#N)=C(N=NCC2=CC=C(OCC3=C(C(=O)[O-])C=CO3)C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 12, 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, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 32, 69, 69, 32, 48, 115, 131, 201, 201, 201, 201, 201, 201, 201, 69, 69, 1, 2, 2, 2, 32, 32, 69, 69, 131, 132, 201, 201, 69, 69] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 26] set([8, 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])
total number of confs: 561
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040958 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040958
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040958/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040958
Building REAL300000040959
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040959'
/scratch/stefan/7769621/working/building/REAL300000040959 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040959

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040959/0 /scratch/stefan/7769621/working/building/REAL300000040959 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1094)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1094
`/scratch/stefan/7769621/working/3D/1094' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CN=NC2=C(C#N)N=C(C)O2)C(OCC(=O)[O-])=C1)

`REAL300000040959.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040959.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040959/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040959 none COC1=CC=C(CN=NC2=C(C#N)N=C(C)O2)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.1', 'N.1', 'N.2', 'C.2', 'C.3', 'O.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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 8, 1, 5, 12, 1, 12, 5, 1, 11, 11, 1, 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, 3, 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: [65, 54, 54, 54, 54, 20, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 125, 199, 201, 201, 54, 65, 65, 65, 54, 54, 19, 20, 2, 2, 2, 199, 199, 54] 201
rigid atoms, others: [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, 34, 35, 36])
total number of confs: 622
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040959 none COC1=CC=C(CN=NC2=C(C#N)N=C(C)O2)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.1', 'N.1', 'N.2', 'C.2', 'C.3', 'O.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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 8, 1, 5, 12, 1, 12, 5, 1, 11, 11, 1, 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, 3, 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: [2, 1, 1, 1, 1, 1, 1, 8, 39, 40, 54, 54, 54, 54, 54, 54, 54, 1, 1, 8, 24, 41, 41, 1, 3, 3, 3, 1, 1, 8, 8, 54, 54, 54, 24, 24, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 17, 18, 23, 36, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 232
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040959 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040959
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040959/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040959
Building REAL300000040960
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040960'
/scratch/stefan/7769621/working/building/REAL300000040960 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040960

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040960/0 /scratch/stefan/7769621/working/building/REAL300000040960 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1095)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1095
`/scratch/stefan/7769621/working/3D/1095' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NCC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)O1)

`REAL300000040960.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040960.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040960/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040960 none CC1=NC(C#N)=C(N=NCC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 12, 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, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 4, 1, 1, 1, 1, 1, 1, 8, 22, 22, 22, 31, 31, 1, 1, 22, 23, 23, 23, 4, 4, 1, 1, 1, 1] 201
rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28])
total number of confs: 142
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040960 none CC1=NC(C#N)=C(N=NCC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 12, 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, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 9, 22, 22, 9, 17, 124, 200, 201, 200, 201, 201, 22, 22, 1, 2, 2, 2, 9, 9, 22, 22, 22, 22] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 633
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040960 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040960
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040960/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040960
Building REAL300000040961
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040961'
/scratch/stefan/7769621/working/building/REAL300000040961 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040961

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040961/0 /scratch/stefan/7769621/working/building/REAL300000040961 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1096)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1096
`/scratch/stefan/7769621/working/3D/1096' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NCC2=C(Br)C=C(C(=O)[O-])N2C)O1)

`REAL300000040961.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040961.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040961/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040961 none CC1=NC(C#N)=C(N=NCC2=C(Br)C=C(C(=O)[O-])N2C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 17, 1, 1, 1, 11, 11, 8, 5, 12, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [78, 78, 78, 78, 78, 78, 49, 49, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 78, 78, 78, 78, 7, 7, 1, 2, 2, 2] 78
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 18, 19, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 20, 21, 22, 23, 24, 25, 27, 28, 29])
total number of confs: 137
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040961 none CC1=NC(C#N)=C(N=NCC2=C(Br)C=C(C(=O)[O-])N2C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 17, 1, 1, 1, 11, 11, 8, 5, 12, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 33, 78, 78, 78, 78, 78, 78, 78, 78, 78, 1, 2, 2, 2, 33, 32, 78, 78, 78, 78] 78
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 175
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040961 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040961
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040961/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040961
Building REAL300000040962
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040962'
/scratch/stefan/7769621/working/building/REAL300000040962 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040962

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040962/0 /scratch/stefan/7769621/working/building/REAL300000040962 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1097)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1097
`/scratch/stefan/7769621/working/3D/1097' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NCC2=CC=C(OCC(=O)[O-])C(Br)=C2)O1)

`REAL300000040962.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040962.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040962/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040962 none CC1=NC(C#N)=C(N=NCC2=CC=C(OCC(=O)[O-])C(Br)=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 12, 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, 3, 7, 7, 2, 2, 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: [50, 50, 50, 50, 50, 50, 49, 49, 8, 1, 1, 1, 1, 1, 1, 7, 17, 25, 25, 1, 1, 1, 50, 50, 50, 50, 8, 8, 1, 1, 17, 17, 1] 201
rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 19, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 157
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040962 none CC1=NC(C#N)=C(N=NCC2=CC=C(OCC(=O)[O-])C(Br)=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 12, 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, 3, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 10, 50, 50, 14, 50, 161, 201, 201, 201, 50, 50, 50, 1, 2, 2, 2, 10, 9, 50, 50, 201, 201, 50] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 585
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040962 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040962
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040962/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040962
Building REAL300000040963
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040963'
/scratch/stefan/7769621/working/building/REAL300000040963 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040963

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040963/0 /scratch/stefan/7769621/working/building/REAL300000040963 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1098)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1098
`/scratch/stefan/7769621/working/3D/1098' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(CN=NC2=C(C#N)N=C(C)O2)C=C1)

`REAL300000040963.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040963.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040963/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040963 none COC1=C2OC(C(=O)[O-])=CC2=C(CN=NC2=C(C#N)N=C(C)O2)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.3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.1', 'N.1', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 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, 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
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, 59, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 59, 59, 2, 2, 2, 201, 201] 201
rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 381
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040963 none COC1=C2OC(C(=O)[O-])=CC2=C(CN=NC2=C(C#N)N=C(C)O2)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.3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.1', 'N.1', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 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, 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
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, 9, 69, 69, 201, 201, 201, 201, 201, 201, 201, 1, 1, 3, 3, 3, 1, 9, 9, 201, 201, 201, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 34, 35, 23, 24, 28] set([0, 32, 33, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 29, 30, 31])
total number of confs: 292
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040963 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040963
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040963/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040963
Building REAL300000040964
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040964'
/scratch/stefan/7769621/working/building/REAL300000040964 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040964

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040964/0 /scratch/stefan/7769621/working/building/REAL300000040964 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1099)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1099
`/scratch/stefan/7769621/working/3D/1099' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NC(C)C2=CC(C(=O)[O-])=CC=C2O)O1)

`REAL300000040964.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040964.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040964/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040964 none CC1=NC(C#N)=C(N=NC(C)C2=CC(C(=O)[O-])=CC=C2O)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [65, 65, 65, 65, 65, 65, 42, 42, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 9, 9, 9, 9, 1, 1, 1, 2] 130
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 32, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 112
number of broken/clashed sets: 53
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040964 none CC1=NC(C#N)=C(N=NC(C)C2=CC(C(=O)[O-])=CC=C2O)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
130  conformations in input
total number of sets (complete confs): 130
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 36, 36, 65, 65, 65, 65, 65, 65, 65, 65, 65, 1, 2, 2, 2, 36, 36, 36, 36, 65, 65, 65, 130] 130
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 295
number of broken/clashed sets: 53
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040964 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040964
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040964/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040964
Building REAL300000040965
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040965'
/scratch/stefan/7769621/working/building/REAL300000040965 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040965

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040965/0 /scratch/stefan/7769621/working/building/REAL300000040965 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1100)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1100
`/scratch/stefan/7769621/working/3D/1100' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(N=NC1=C(C#N)N=C(C)O1)C1=CC(C(=O)[O-])=CC=C1F)

`REAL300000040965.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040965.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040965/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040965 none CCC(N=NC1=C(C#N)N=C(C)O1)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.1', 'N.1', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 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, 2, 2, 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: [16, 10, 1, 10, 62, 62, 131, 131, 131, 131, 131, 131, 131, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 19, 19, 19, 19, 19, 10, 131, 131, 131, 1, 1, 1] 131
rigid atoms, others: [32, 33, 2, 34, 13, 14, 15, 16, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 262
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040965 none CCC(N=NC1=C(C#N)N=C(C)O1)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.1', 'N.1', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 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, 2, 2, 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: [66, 50, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 131, 131, 131, 131, 131, 131, 131, 131, 131, 73, 73, 73, 73, 73, 50, 2, 2, 2, 131, 131, 131] 131
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 13, 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: 436
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040965 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040965
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040965/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040965
Building REAL300000040966
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040966'
/scratch/stefan/7769621/working/building/REAL300000040966 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040966

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040966/0 /scratch/stefan/7769621/working/building/REAL300000040966 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1101)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1101
`/scratch/stefan/7769621/working/3D/1101' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NCC2=C3C=CC(C(=O)[O-])=CC3=NN2)O1)

`REAL300000040966.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040966.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040966/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040966 none CC1=NC(C#N)=C(N=NCC2=C3C=CC(C(=O)[O-])=CC3=NN2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 3, 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: [112, 112, 112, 112, 112, 112, 65, 64, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 112, 112, 112, 112, 9, 9, 1, 1, 1, 1] 112
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 22, 23, 24, 25, 26, 27])
total number of confs: 180
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040966 none CC1=NC(C#N)=C(N=NCC2=C3C=CC(C(=O)[O-])=CC3=NN2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
112  conformations in input
total number of sets (complete confs): 112
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 43, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 1, 2, 2, 2, 43, 43, 112, 112, 112, 112] 112
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 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/7769621/working/building/REAL300000040966 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040966
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040966/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040966
Building REAL300000040967
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040967'
/scratch/stefan/7769621/working/building/REAL300000040967 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040967

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040967/0 /scratch/stefan/7769621/working/building/REAL300000040967 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1102)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1102
`/scratch/stefan/7769621/working/3D/1102' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NC(C)C2=CC=C(C(=O)[O-])C(F)=C2)O1)

`REAL300000040967.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040967.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040967/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040967 none CC1=NC(C#N)=C(N=NC(C)C2=CC=C(C(=O)[O-])C(F)=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 12, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [141, 141, 141, 141, 141, 141, 70, 70, 13, 1, 13, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 141, 141, 141, 141, 13, 13, 13, 13, 1, 1, 1] 141
rigid atoms, others: [9, 11, 12, 13, 14, 15, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 222
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040967 none CC1=NC(C#N)=C(N=NC(C)C2=CC=C(C(=O)[O-])C(F)=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 12, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 48, 48, 141, 141, 141, 141, 141, 141, 141, 141, 141, 1, 2, 2, 2, 48, 48, 48, 48, 141, 141, 141] 141
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 289
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040967 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040967
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040967/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040967
Building REAL300000040968
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040968'
/scratch/stefan/7769621/working/building/REAL300000040968 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000040968

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040968/0 /scratch/stefan/7769621/working/building/REAL300000040968 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1103)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1103
`/scratch/stefan/7769621/working/3D/1103' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(CN=NC2=C(C#N)N=C(C)O2)=C([N+](=O)[O-])C=C1OCC(=O)[O-])

`REAL300000040968.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040968.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040968/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040968 none COC1=CC(CN=NC2=C(C#N)N=C(C)O2)=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.3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.1', 'N.1', 'N.2', 'C.2', 'C.3', 'O.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']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 8, 1, 5, 12, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 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, 3, 7, 7, 3, 3, 7, 7, 3, 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: [89, 48, 48, 48, 40, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48, 48, 147, 197, 201, 201, 89, 89, 89, 48, 39, 40, 2, 2, 2, 48, 197, 197] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 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: 662
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040968 none COC1=CC(CN=NC2=C(C#N)N=C(C)O2)=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.3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.1', 'N.1', 'N.2', 'C.2', 'C.3', 'O.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']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 8, 1, 5, 12, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 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, 3, 7, 7, 3, 3, 7, 7, 3, 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: [3, 1, 1, 1, 1, 1, 4, 16, 16, 48, 48, 48, 48, 48, 48, 48, 1, 1, 2, 2, 1, 1, 1, 9, 19, 33, 33, 4, 4, 4, 1, 4, 4, 48, 48, 48, 1, 19, 19] 201
rigid atoms, others: [1, 2, 3, 4, 5, 16, 17, 20, 21, 22, 36, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 185
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040968 /scratch/stefan/7769621/working /scratch/stefan/7769621
mkdir: created directory `1'
/scratch/stefan/7769621/working/building/REAL300000040968/1 /scratch/stefan/7769621/working/building/REAL300000040968 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 1 (index: 1104)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1104
`/scratch/stefan/7769621/working/3D/1104' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=N[N-]C2=C(C#N)N=C(C)O2)=C([N+](=O)[O-])C=C1OCC(=O)[O-])

`REAL300000040968.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000040968.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040968/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040968 none COC1=CC(C=N[N-]C2=C(C#N)N=C(C)O2)=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.2', 'C.2', 'C.2', 'C.1', 'N.1', 'N.2', 'C.2', 'C.3', 'O.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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 5, 12, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 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, 3, 7, 7, 3, 3, 7, 7, 3, 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: [145, 86, 86, 86, 42, 42, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 86, 86, 86, 192, 201, 201, 201, 145, 145, 145, 86, 42, 2, 2, 2, 86, 201, 201] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 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: 443
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040968 none COC1=CC(C=N[N-]C2=C(C#N)N=C(C)O2)=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.2', 'C.2', 'C.2', 'C.1', 'N.1', 'N.2', 'C.2', 'C.3', 'O.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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 5, 12, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 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, 3, 7, 7, 3, 3, 7, 7, 3, 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: [3, 1, 1, 1, 1, 1, 5, 5, 21, 86, 86, 86, 86, 86, 86, 86, 1, 1, 2, 2, 1, 1, 1, 9, 13, 19, 19, 4, 4, 4, 1, 5, 86, 86, 86, 1, 13, 13] 201
rigid atoms, others: [1, 2, 3, 4, 5, 16, 17, 35, 20, 21, 22, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 36, 37])
total number of confs: 178
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040968 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040968
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
1: /scratch/stefan/7769621/working/building/REAL300000040968/1.*
0: /scratch/stefan/7769621/working/building/REAL300000040968/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040968
Building REAL300000040969
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040969'
/scratch/stefan/7769621/working/building/REAL300000040969 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040969

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040969/0 /scratch/stefan/7769621/working/building/REAL300000040969 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1105)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1105
`/scratch/stefan/7769621/working/3D/1105' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NCC2=CC(C(F)(F)F)=CC=C2N(C)CC(=O)[O-])O1)

`REAL300000040969.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040969.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040969/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040969 none CC1=NC(C#N)=C(N=NCC2=CC(C(F)(F)F)=CC=C2N(C)CC(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 1, 11, 11, 12, 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, 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: [106, 106, 106, 106, 106, 106, 55, 54, 8, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 4, 4, 15, 23, 23, 106, 106, 106, 106, 8, 8, 1, 1, 1, 4, 4, 4, 15, 15] 201
rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39])
total number of confs: 248
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040969 none CC1=NC(C#N)=C(N=NCC2=CC(C(F)(F)F)=CC=C2N(C)CC(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 1, 11, 11, 12, 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, 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, 1, 1, 1, 7, 7, 42, 106, 106, 106, 106, 106, 106, 103, 106, 106, 106, 115, 115, 201, 201, 201, 1, 2, 2, 2, 42, 42, 106, 105, 106, 115, 115, 115, 201, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 26] set([8, 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])
total number of confs: 677
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040969 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040969
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040969/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040969
Building REAL300000040970
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040970'
/scratch/stefan/7769621/working/building/REAL300000040970 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040970

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040970/0 /scratch/stefan/7769621/working/building/REAL300000040970 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1106)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1106
`/scratch/stefan/7769621/working/3D/1106' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NC(C)C2=CC=C(OC3=CC=C(C(=O)[O-])C=C3)C=C2)O1)

`REAL300000040970.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040970.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040970/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040970 none CC1=NC(C#N)=C(N=NC(C)C2=CC=C(OC3=CC=C(C(=O)[O-])C=C3)C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 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, 3, 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]
0  hydrogens need rotated
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, 167, 167, 62, 19, 62, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 201, 201, 201, 201, 62, 62, 62, 62, 19, 19, 1, 1, 1, 1, 19, 19] 201
rigid atoms, others: [37, 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, 41, 42])
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: REAL300000040970 none CC1=NC(C#N)=C(N=NC(C)C2=CC=C(OC3=CC=C(C(=O)[O-])C=C3)C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 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, 3, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [49, 49, 49, 49, 49, 49, 31, 31, 7, 1, 7, 1, 1, 1, 1, 1, 9, 19, 19, 9, 11, 19, 19, 19, 19, 1, 1, 49, 49, 49, 49, 7, 7, 7, 7, 1, 1, 19, 19, 19, 19, 1, 1] 201
rigid atoms, others: [35, 36, 9, 42, 11, 12, 13, 14, 15, 41, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40])
total number of confs: 155
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040970 none CC1=NC(C#N)=C(N=NC(C)C2=CC=C(OC3=CC=C(C(=O)[O-])C=C3)C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 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, 3, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 24, 24, 49, 49, 25, 49, 184, 201, 201, 184, 184, 201, 201, 201, 201, 49, 49, 1, 2, 2, 2, 24, 24, 24, 24, 49, 49, 201, 201, 201, 201, 49, 49] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 527
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040970 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040970
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040970/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040970
Building REAL300000040971
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040971'
/scratch/stefan/7769621/working/building/REAL300000040971 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040971

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040971/0 /scratch/stefan/7769621/working/building/REAL300000040971 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1107)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1107
`/scratch/stefan/7769621/working/3D/1107' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(CN=NC2=C(C#N)N=C(C)O2)=CC=C1OCCC(=O)[O-])

`REAL300000040971.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040971.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040971/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040971 none COC1=CC(CN=NC2=C(C#N)N=C(C)O2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.1', 'N.1', 'N.2', 'C.2', 'C.3', 'O.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']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 1, 12, 5, 5, 1, 11, 11, 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, 3, 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: [77, 39, 39, 39, 8, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 132, 189, 189, 201, 190, 77, 77, 77, 39, 8, 7, 2, 2, 2, 39, 39, 189, 189, 189, 189] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 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: 634
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040971 none COC1=CC(CN=NC2=C(C#N)N=C(C)O2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.1', 'N.1', 'N.2', 'C.2', 'C.3', 'O.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']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 1, 12, 5, 5, 1, 11, 11, 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, 3, 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: [3, 1, 1, 1, 1, 1, 6, 38, 38, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 5, 9, 9, 17, 15, 3, 3, 3, 1, 6, 6, 39, 39, 39, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [19, 1, 2, 3, 4, 5, 34, 16, 17, 18, 35, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 36, 37, 38, 39])
total number of confs: 113
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040971 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040971
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040971/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040971
Building REAL300000040972
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040972'
/scratch/stefan/7769621/working/building/REAL300000040972 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040972

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040972/0 /scratch/stefan/7769621/working/building/REAL300000040972 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1108)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1108
`/scratch/stefan/7769621/working/3D/1108' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NCC2=CC=C(C(=O)[O-])C=C2Cl)O1)

`REAL300000040972.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040972.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040972/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040972 none CC1=NC(C#N)=C(N=NCC2=CC=C(C(=O)[O-])C=C2Cl)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 12, 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, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [90, 90, 90, 90, 90, 90, 58, 57, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 90, 90, 90, 90, 8, 8, 1, 1, 1] 90
rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25])
total number of confs: 144
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040972 none CC1=NC(C#N)=C(N=NCC2=CC=C(C(=O)[O-])C=C2Cl)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 12, 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, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 32, 90, 90, 32, 52, 90, 90, 90, 90, 90, 1, 2, 2, 2, 32, 32, 90, 90, 90] 90
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 455
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040972 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040972
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040972/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040972
Building REAL300000040973
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040973'
/scratch/stefan/7769621/working/building/REAL300000040973 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040973

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040973/0 /scratch/stefan/7769621/working/building/REAL300000040973 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1109)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1109
`/scratch/stefan/7769621/working/3D/1109' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NC(C)C2=CC(C(=O)[O-])=C(C)N=C2C)O1)

`REAL300000040973.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040973.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040973/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040973 none CC1=NC(C#N)=C(N=NC(C)C2=CC(C(=O)[O-])=C(C)N=C2C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 12, 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, 2, 2, 7, 7, 3, 7, 7, 3, 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, 76, 76, 76, 37, 37, 5, 1, 5, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 76, 76, 76, 76, 5, 5, 5, 5, 1, 2, 2, 2, 2, 2, 2] 76
rigid atoms, others: [9, 11, 12, 13, 14, 17, 18, 19, 20, 21, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36])
total number of confs: 132
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040973 none CC1=NC(C#N)=C(N=NC(C)C2=CC(C(=O)[O-])=C(C)N=C2C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 12, 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, 2, 2, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
76  conformations in input
total number of sets (complete confs): 76
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 39, 39, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 1, 2, 2, 2, 39, 39, 39, 39, 76, 76, 76, 76, 76, 76, 76] 76
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 188
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040973 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040973
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040973/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040973
Building REAL300000040974
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040974'
/scratch/stefan/7769621/working/building/REAL300000040974 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040974

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040974/0 /scratch/stefan/7769621/working/building/REAL300000040974 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1110)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1110
`/scratch/stefan/7769621/working/3D/1110' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NCC2=CC=C(OC(C)C(=O)[O-])C=C2)O1)

`REAL300000040974.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040974.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040974/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040974 none CC1=NC(C#N)=C(N=NCC2=CC=C(OC(C)C(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 12, 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, 3, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [34, 34, 34, 34, 34, 34, 30, 30, 4, 1, 1, 1, 1, 1, 1, 9, 24, 24, 35, 35, 1, 1, 34, 35, 35, 35, 4, 4, 1, 1, 24, 24, 24, 24, 1, 1] 201
rigid atoms, others: [34, 35, 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])
total number of confs: 173
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040974 none CC1=NC(C#N)=C(N=NCC2=CC=C(OC(C)C(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 12, 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, 3, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 11, 34, 34, 11, 20, 130, 201, 201, 201, 201, 34, 34, 1, 2, 2, 2, 11, 11, 34, 34, 201, 201, 201, 201, 34, 34] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 648
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040974 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040974
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040974/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040974
Building REAL300000040975
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040975'
/scratch/stefan/7769621/working/building/REAL300000040975 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040975

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040975/0 /scratch/stefan/7769621/working/building/REAL300000040975 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1111)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1111
`/scratch/stefan/7769621/working/3D/1111' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NCC2=CN(CC(=O)[O-])C3=CC=CC=C23)O1)

`REAL300000040975.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040975.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040975/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040975 none CC1=NC(C#N)=C(N=NCC2=CN(CC(=O)[O-])C3=CC=CC=C23)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 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, 2, 2, 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: [81, 81, 81, 81, 81, 81, 63, 62, 9, 1, 1, 1, 1, 1, 8, 12, 12, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 9, 9, 1, 8, 8, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 23, 24, 25, 26, 27, 28, 30, 31])
total number of confs: 166
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040975 none CC1=NC(C#N)=C(N=NCC2=CN(CC(=O)[O-])C3=CC=CC=C23)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 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, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 20, 81, 81, 81, 201, 201, 201, 81, 81, 81, 81, 81, 81, 1, 2, 2, 2, 19, 20, 81, 201, 201, 81, 81, 81, 81] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 23] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 667
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040975 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040975
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040975/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040975
Building REAL300000040976
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040976'
/scratch/stefan/7769621/working/building/REAL300000040976 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040976

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040976/0 /scratch/stefan/7769621/working/building/REAL300000040976 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1112)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1112
`/scratch/stefan/7769621/working/3D/1112' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NC(C)C2=CC=CC(OCCCC(=O)[O-])=C2)O1)

`REAL300000040976.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040976.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040976/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040976 none CC1=NC(C#N)=C(N=NC(C)C2=CC=CC(OCCCC(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', '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', '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, 8, 1, 1, 8, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 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, 7, 7, 7, 7, 3, 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: [30, 30, 30, 30, 30, 30, 27, 27, 7, 1, 7, 1, 1, 1, 1, 1, 1, 7, 15, 16, 26, 44, 44, 1, 30, 30, 30, 30, 7, 7, 7, 7, 1, 1, 1, 15, 15, 16, 16, 26, 26, 1] 201
rigid atoms, others: [32, 33, 34, 9, 11, 12, 13, 14, 15, 16, 41, 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, 35, 36, 37, 38, 39, 40])
total number of confs: 231
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040976 none CC1=NC(C#N)=C(N=NC(C)C2=CC=CC(OCCCC(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', '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', '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, 8, 1, 1, 8, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 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, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 30, 30, 30, 30, 30, 117, 147, 147, 201, 201, 201, 30, 1, 2, 2, 2, 10, 10, 10, 10, 30, 30, 30, 147, 147, 147, 147, 201, 201, 30] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 655
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040976 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040976
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040976/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040976
Building REAL300000040977
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040977'
/scratch/stefan/7769621/working/building/REAL300000040977 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040977

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040977/0 /scratch/stefan/7769621/working/building/REAL300000040977 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1113)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1113
`/scratch/stefan/7769621/working/3D/1113' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NC(C)CCC2=CC=C(OC(C)C(=O)[O-])C=C2)O1)

`REAL300000040977.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040977.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040977/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040977 none CC1=NC(C#N)=C(N=NC(C)CCC2=CC=C(OC(C)C(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 12, 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, 3, 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: [51, 51, 51, 51, 51, 51, 37, 37, 9, 3, 9, 2, 1, 1, 1, 1, 1, 1, 11, 24, 24, 32, 32, 1, 1, 51, 51, 51, 51, 9, 9, 9, 9, 3, 3, 2, 2, 1, 1, 24, 24, 24, 24, 1, 1] 201
rigid atoms, others: [37, 38, 44, 43, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42])
total number of confs: 191
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040977 none CC1=NC(C#N)=C(N=NC(C)CCC2=CC=C(OC(C)C(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 12, 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, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 20, 20, 46, 51, 51, 51, 51, 51, 166, 201, 201, 201, 201, 51, 51, 1, 2, 2, 2, 20, 20, 20, 20, 49, 49, 50, 51, 51, 51, 201, 201, 201, 201, 51, 51] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 578
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040977 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040977
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040977/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040977
Building REAL300000040978
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040978'
/scratch/stefan/7769621/working/building/REAL300000040978 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040978

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040978/0 /scratch/stefan/7769621/working/building/REAL300000040978 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1114)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1114
`/scratch/stefan/7769621/working/3D/1114' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NC(C)CCC2=CC=C(OCC(=O)[O-])C=C2)O1)

`REAL300000040978.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040978.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040978/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040978 none CC1=NC(C#N)=C(N=NC(C)CCC2=CC=C(OCC(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', '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', '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, 8, 1, 1, 8, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 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, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 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: [48, 48, 48, 48, 48, 48, 34, 34, 10, 4, 10, 2, 1, 1, 1, 1, 1, 1, 6, 19, 31, 31, 1, 1, 48, 48, 48, 48, 10, 10, 10, 10, 4, 4, 2, 2, 1, 1, 19, 19, 1, 1] 201
rigid atoms, others: [36, 37, 40, 41, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39])
total number of confs: 183
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040978 none CC1=NC(C#N)=C(N=NC(C)CCC2=CC=C(OCC(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', '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', '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, 8, 1, 1, 8, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 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, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 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, 1, 1, 1, 4, 4, 21, 21, 42, 48, 48, 48, 48, 48, 133, 201, 201, 201, 48, 48, 1, 2, 2, 2, 21, 21, 21, 21, 45, 45, 47, 48, 48, 48, 201, 201, 48, 48] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 680
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040978 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040978
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040978/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040978
Building REAL300000040979
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040979'
/scratch/stefan/7769621/working/building/REAL300000040979 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040979

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040979/0 /scratch/stefan/7769621/working/building/REAL300000040979 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1115)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1115
`/scratch/stefan/7769621/working/3D/1115' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NC(C)C2=CC=CC(OC(C)C(=O)[O-])=C2)O1)

`REAL300000040979.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040979.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040979/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040979 none CC1=NC(C#N)=C(N=NC(C)C2=CC=CC(OC(C)C(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 12, 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, 3, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [42, 42, 42, 42, 42, 42, 35, 35, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 26, 26, 37, 37, 1, 42, 42, 42, 42, 7, 7, 7, 7, 1, 1, 1, 26, 26, 26, 26, 1] 201
rigid atoms, others: [32, 33, 38, 9, 11, 12, 13, 14, 15, 16, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37])
total number of confs: 187
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040979 none CC1=NC(C#N)=C(N=NC(C)C2=CC=CC(OC(C)C(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 12, 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, 3, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 14, 42, 42, 42, 42, 42, 144, 201, 201, 201, 201, 42, 1, 2, 2, 2, 14, 14, 14, 14, 42, 42, 42, 201, 201, 201, 201, 42] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 23] set([8, 9, 10, 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: 529
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040979 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040979
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040979/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040979
Building REAL300000040980
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040980'
/scratch/stefan/7769621/working/building/REAL300000040980 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040980

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040980/0 /scratch/stefan/7769621/working/building/REAL300000040980 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1116)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1116
`/scratch/stefan/7769621/working/3D/1116' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NC(C)CCC2=CC=C(OCCC(=O)[O-])C=C2)O1)

`REAL300000040980.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040980.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040980/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040980 none CC1=NC(C#N)=C(N=NC(C)CCC2=CC=C(OCCC(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 12, 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, 3, 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: [55, 55, 55, 55, 55, 55, 34, 34, 9, 4, 9, 3, 1, 1, 1, 1, 1, 1, 6, 16, 16, 26, 24, 1, 1, 55, 55, 55, 55, 9, 9, 9, 9, 4, 4, 3, 3, 1, 1, 16, 16, 16, 16, 1, 1] 201
rigid atoms, others: [37, 38, 44, 43, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42])
total number of confs: 182
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040980 none CC1=NC(C#N)=C(N=NC(C)CCC2=CC=C(OCCC(=O)[O-])C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 12, 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, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 49, 54, 55, 55, 54, 55, 187, 201, 201, 201, 200, 55, 55, 1, 2, 2, 2, 27, 27, 27, 27, 52, 52, 54, 54, 55, 55, 201, 201, 201, 201, 55, 55] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 487
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040980 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040980
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040980/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040980
Building REAL300000040981
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040981'
/scratch/stefan/7769621/working/building/REAL300000040981 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040981

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040981/0 /scratch/stefan/7769621/working/building/REAL300000040981 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1117)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1117
`/scratch/stefan/7769621/working/3D/1117' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(N=NC1=C(C#N)N=C(C)O1)C1=CC=C(OCCCCC(=O)[O-])C=C1)

`REAL300000040981.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040981.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040981/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040981 none CCC(N=NC1=C(C#N)N=C(C)O1)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.1', 'N.1', 'N.2', 'C.2', 'C.3', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 8, 8, 1, 5, 12, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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]
0  hydrogens 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, 1, 4, 11, 11, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 6, 10, 24, 30, 52, 59, 62, 1, 1, 5, 5, 5, 5, 5, 4, 16, 16, 16, 1, 1, 10, 10, 23, 23, 30, 30, 51, 51, 1, 1] 201
rigid atoms, others: [2, 36, 37, 13, 14, 15, 16, 17, 46, 25, 26, 47] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 311
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040981 none CCC(N=NC1=C(C#N)N=C(C)O1)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.1', 'N.1', 'N.2', 'C.2', 'C.3', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 8, 8, 1, 5, 12, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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]
0  hydrogens 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, 9, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 16, 16, 9, 10, 55, 78, 123, 138, 187, 196, 201, 16, 16, 13, 13, 13, 13, 13, 9, 2, 2, 2, 16, 16, 74, 76, 123, 123, 138, 138, 187, 187, 16, 16] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 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])
total number of confs: 866
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040981 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040981
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040981/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040981
Building REAL300000040982
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040982'
/scratch/stefan/7769621/working/building/REAL300000040982 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040982

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040982/0 /scratch/stefan/7769621/working/building/REAL300000040982 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1118)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1118
`/scratch/stefan/7769621/working/3D/1118' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NC2CC(C(=O)[O-])(C3=CC=CC=C3)C2)O1)

`REAL300000040982.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040982.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040982/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040982 none CC1=NC(C#N)=C(N=NC2CC(C(=O)[O-])(C3=CC=CC=C3)C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 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, 36, 36, 5, 5, 5, 1, 5, 9, 9, 1, 1, 1, 1, 1, 1, 5, 55, 55, 55, 55, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5] 55
rigid atoms, others: [32, 33, 11, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35])
total number of confs: 95
number of broken/clashed sets: 55
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040982 none CC1=NC(C#N)=C(N=NC2CC(C(=O)[O-])(C3=CC=CC=C3)C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 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: [34, 34, 34, 34, 34, 34, 13, 13, 1, 1, 1, 1, 1, 3, 3, 1, 5, 5, 2, 5, 5, 1, 34, 34, 34, 34, 1, 1, 1, 5, 5, 2, 5, 5, 1, 1] 55
rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 15, 21, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31, 32, 33])
total number of confs: 64
number of broken/clashed sets: 55
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040982 none CC1=NC(C#N)=C(N=NC2CC(C(=O)[O-])(C3=CC=CC=C3)C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 34, 34, 34, 52, 52, 34, 55, 55, 44, 55, 55, 34, 1, 2, 2, 2, 34, 34, 34, 55, 55, 45, 55, 55, 34, 34] 55
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 225
number of broken/clashed sets: 55
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040982 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040982
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040982/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040982
Building REAL300000040983
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040983'
/scratch/stefan/7769621/working/building/REAL300000040983 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040983

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040983/0 /scratch/stefan/7769621/working/building/REAL300000040983 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1119)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1119
`/scratch/stefan/7769621/working/3D/1119' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NC(C)[C@@H]2C[C@H](CC(=O)[O-])C2(C)C)O1)

`REAL300000040983.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040983.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040983/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040983 none CC1=NC(C#N)=C(N=NC(C)[C@@H]2C[C@H](CC(=O)[O-])C2(C)C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', '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', '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, 8, 1, 1, 8, 1, 8, 8, 5, 5, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 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, 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]
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: [46, 46, 46, 46, 46, 46, 25, 25, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 12, 12, 1, 1, 1, 46, 46, 46, 46, 4, 4, 4, 4, 1, 1, 7, 7, 2, 2, 2, 2, 2, 2] 63
rigid atoms, others: [32, 9, 11, 12, 13, 14, 15, 16, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 120
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040983 none CC1=NC(C#N)=C(N=NC(C)[C@@H]2C[C@H](CC(=O)[O-])C2(C)C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', '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', '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, 8, 1, 1, 8, 1, 8, 8, 5, 5, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 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, 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]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31, 46, 46, 46, 46, 46, 63, 63, 63, 46, 46, 46, 1, 2, 2, 2, 31, 31, 31, 31, 46, 46, 63, 63, 46, 46, 46, 46, 46, 46] 63
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 23] set([8, 9, 10, 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, 39, 40])
total number of confs: 250
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040983 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040983
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040983/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040983
Building REAL300000040984
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040984'
/scratch/stefan/7769621/working/building/REAL300000040984 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040984

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040984/0 /scratch/stefan/7769621/working/building/REAL300000040984 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1120)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1120
`/scratch/stefan/7769621/working/3D/1120' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(C)N=NC2=C(C#N)N=C(C)O2)=CC=C1OCCCC(=O)[O-])

`REAL300000040984.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040984.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040984/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040984 none COC1=CC(C(C)N=NC2=C(C#N)N=C(C)O2)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.1', 'N.1', 'N.2', 'C.2', 'C.3', 'O.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']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 8, 8, 1, 5, 12, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7]
0  hydrogens 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, 29, 29, 29, 8, 3, 8, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 94, 171, 171, 201, 201, 201, 50, 50, 50, 29, 8, 8, 8, 8, 2, 2, 2, 29, 29, 171, 171, 171, 171, 201, 201] 201
rigid atoms, others: [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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 709
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040984 none COC1=CC(C(C)N=NC2=C(C#N)N=C(C)O2)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.1', 'N.1', 'N.2', 'C.2', 'C.3', 'O.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']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 8, 8, 1, 5, 12, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7]
0  hydrogens 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, 27, 27, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 7, 14, 14, 25, 35, 35, 3, 3, 3, 1, 7, 7, 7, 7, 29, 29, 29, 1, 1, 14, 14, 14, 14, 25, 25] 201
rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 17, 18, 19, 20, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45])
total number of confs: 194
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040984 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040984
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040984/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040984
Building REAL300000040985
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040985'
/scratch/stefan/7769621/working/building/REAL300000040985 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040985

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040985/0 /scratch/stefan/7769621/working/building/REAL300000040985 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1121)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1121
`/scratch/stefan/7769621/working/3D/1121' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NC2CC(C(=O)[O-])(C3=CC=CC(Cl)=C3)C2)O1)

`REAL300000040985.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040985.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040985/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040985 none CC1=NC(C#N)=C(N=NC2CC(C(=O)[O-])(C3=CC=CC(Cl)=C3)C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', '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', 'Cl', 'C.ar', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [73, 73, 73, 73, 73, 73, 47, 47, 12, 12, 12, 1, 12, 18, 18, 1, 1, 1, 1, 1, 1, 1, 12, 73, 73, 73, 73, 12, 12, 12, 1, 1, 1, 1, 12, 12] 73
rigid atoms, others: [32, 33, 11, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 135
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040985 none CC1=NC(C#N)=C(N=NC2CC(C(=O)[O-])(C3=CC=CC(Cl)=C3)C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', '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', 'Cl', 'C.ar', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [29, 29, 29, 29, 29, 29, 9, 9, 1, 1, 1, 1, 1, 3, 3, 1, 12, 12, 11, 12, 12, 12, 1, 29, 29, 29, 29, 1, 1, 1, 12, 12, 11, 12, 1, 1] 73
rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 15, 22, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 58
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040985 none CC1=NC(C#N)=C(N=NC2CC(C(=O)[O-])(C3=CC=CC(Cl)=C3)C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', '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', 'Cl', 'C.ar', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 29, 29, 29, 37, 37, 29, 73, 73, 73, 73, 73, 73, 29, 1, 2, 2, 2, 29, 29, 29, 73, 73, 73, 73, 29, 29] 73
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 23] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 166
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040985 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040985
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040985/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040985
Building REAL300000040986
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040986'
/scratch/stefan/7769621/working/building/REAL300000040986 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040986

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040986/0 /scratch/stefan/7769621/working/building/REAL300000040986 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1122)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1122
`/scratch/stefan/7769621/working/3D/1122' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NC2CC(C(=O)[O-])(C3=CC=CC(Br)=C3)C2)O1)

`REAL300000040986.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040986.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040986/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040986 none CC1=NC(C#N)=C(N=NC2CC(C(=O)[O-])(C3=CC=CC(Br)=C3)C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', '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', 'Br', 'C.ar', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [73, 73, 73, 73, 73, 73, 46, 46, 12, 12, 12, 1, 12, 18, 18, 1, 1, 1, 1, 1, 1, 1, 12, 73, 73, 73, 73, 12, 12, 12, 1, 1, 1, 1, 12, 12] 73
rigid atoms, others: [32, 33, 11, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 136
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040986 none CC1=NC(C#N)=C(N=NC2CC(C(=O)[O-])(C3=CC=CC(Br)=C3)C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', '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', 'Br', 'C.ar', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [29, 29, 29, 29, 29, 29, 9, 9, 1, 1, 1, 1, 1, 3, 3, 1, 12, 12, 11, 12, 12, 12, 1, 29, 29, 29, 29, 1, 1, 1, 12, 12, 11, 12, 1, 1] 73
rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 15, 22, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 58
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040986 none CC1=NC(C#N)=C(N=NC2CC(C(=O)[O-])(C3=CC=CC(Br)=C3)C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', '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', 'Br', 'C.ar', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 29, 29, 29, 37, 37, 29, 73, 73, 73, 73, 73, 73, 29, 1, 2, 2, 2, 29, 29, 29, 73, 73, 73, 73, 29, 29] 73
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 23] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 167
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040986 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040986
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040986/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040986
Building REAL300000040987
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040987'
/scratch/stefan/7769621/working/building/REAL300000040987 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040987

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040987/0 /scratch/stefan/7769621/working/building/REAL300000040987 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1123)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1123
`/scratch/stefan/7769621/working/3D/1123' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NC2CCCC3=CC(C(=O)[O-])=CC=C32)O1)

`REAL300000040987.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040987.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040987/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040987 none CC1=NC(C#N)=C(N=NC2CCCC3=CC(C(=O)[O-])=CC=C32)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 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, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 14, 14, 14, 14, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 14
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 22, 23, 24, 25])
total number of confs: 24
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040987 none CC1=NC(C#N)=C(N=NC2CCCC3=CC(C(=O)[O-])=CC=C32)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 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, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 2, 2, 2, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 14
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 34
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040987 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040987
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040987/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040987
Building REAL300000040988
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040988'
/scratch/stefan/7769621/working/building/REAL300000040988 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040988

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040988/0 /scratch/stefan/7769621/working/building/REAL300000040988 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1124)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1124
`/scratch/stefan/7769621/working/3D/1124' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NC(C)C2=CC(Br)=CC=C2OCC(=O)[O-])O1)

`REAL300000040988.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040988.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040988/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040988 none CC1=NC(C#N)=C(N=NC(C)C2=CC(Br)=CC=C2OCC(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 12, 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, 3, 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: [44, 44, 44, 44, 44, 44, 27, 27, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 29, 50, 50, 44, 44, 44, 44, 5, 5, 5, 5, 1, 1, 1, 29, 29] 201
rigid atoms, others: [32, 33, 9, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35])
total number of confs: 234
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040988 none CC1=NC(C#N)=C(N=NC(C)C2=CC(Br)=CC=C2OCC(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 12, 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, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 44, 44, 44, 23, 44, 44, 44, 104, 201, 201, 201, 1, 2, 2, 2, 23, 23, 23, 23, 44, 44, 44, 201, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 23] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 742
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040988 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040988
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040988/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040988
Building REAL300000040989
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040989'
/scratch/stefan/7769621/working/building/REAL300000040989 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040989

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040989/0 /scratch/stefan/7769621/working/building/REAL300000040989 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1125)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1125
`/scratch/stefan/7769621/working/3D/1125' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NC(C)C2=C(CC(=O)[O-])C3=CC=C(C)C=C3O2)O1)

`REAL300000040989.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040989.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040989/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040989 none CC1=NC(C#N)=C(N=NC(C)C2=C(CC(=O)[O-])C3=CC=C(C)C=C3O2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 12, 12, 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, 2, 2, 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
134  conformations in input
total number of sets (complete confs): 134
using faster count positions algorithm for large data
unique positions, atoms: [90, 90, 90, 90, 90, 90, 46, 46, 6, 1, 6, 1, 1, 1, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 90, 90, 90, 90, 6, 6, 6, 6, 2, 2, 1, 1, 2, 2, 2, 1] 134
rigid atoms, others: [35, 36, 40, 9, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39])
total number of confs: 165
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040989 none CC1=NC(C#N)=C(N=NC(C)C2=C(CC(=O)[O-])C3=CC=C(C)C=C3O2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 12, 12, 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, 2, 2, 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
134  conformations in input
total number of sets (complete confs): 134
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 35, 35, 90, 90, 134, 134, 134, 90, 90, 90, 90, 90, 90, 90, 90, 1, 2, 2, 2, 35, 35, 35, 35, 134, 134, 90, 90, 90, 90, 90, 90] 134
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 457
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040989 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040989
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040989/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040989
Building REAL300000040990
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040990'
/scratch/stefan/7769621/working/building/REAL300000040990 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040990

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040990/0 /scratch/stefan/7769621/working/building/REAL300000040990 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1126)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1126
`/scratch/stefan/7769621/working/3D/1126' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NCC2=CC=CC(C(=O)[O-])=C2Cl)O1)

`REAL300000040990.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040990.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040990/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040990 none CC1=NC(C#N)=C(N=NCC2=CC=CC(C(=O)[O-])=C2Cl)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 12, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [113, 113, 113, 113, 113, 113, 60, 60, 8, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 113, 113, 113, 113, 8, 8, 1, 1, 1] 113
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 20, 21, 22, 23, 24, 25])
total number of confs: 176
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040990 none CC1=NC(C#N)=C(N=NCC2=CC=CC(C(=O)[O-])=C2Cl)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 12, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 39, 113, 113, 113, 113, 113, 113, 113, 113, 113, 1, 2, 2, 2, 39, 39, 113, 113, 113] 113
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 237
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040990 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040990
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040990/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040990
Building REAL300000040991
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040991'
/scratch/stefan/7769621/working/building/REAL300000040991 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040991

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040991/0 /scratch/stefan/7769621/working/building/REAL300000040991 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1127)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1127
`/scratch/stefan/7769621/working/3D/1127' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NC2CCCCC3=CC(C(=O)[O-])=CC=C32)O1)

`REAL300000040991.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040991.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040991/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040991 none CC1=NC(C#N)=C(N=NC2CCCCC3=CC(C(=O)[O-])=CC=C32)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 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, 2, 2, 7, 7, 7, 3, 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, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 11
rigid atoms, others: [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] set([0, 1, 2, 3, 4, 5, 6, 7, 23, 24, 25, 26])
total number of confs: 16
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040991 none CC1=NC(C#N)=C(N=NC2CCCCC3=CC(C(=O)[O-])=CC=C32)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 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, 2, 2, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 11
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 23] set([8, 9, 10, 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: 31
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040991 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040991
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040991/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040991
Building REAL300000040992
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040992'
/scratch/stefan/7769621/working/building/REAL300000040992 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040992

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040992/0 /scratch/stefan/7769621/working/building/REAL300000040992 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1128)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1128
`/scratch/stefan/7769621/working/3D/1128' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NCC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)O1)

`REAL300000040992.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040992.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040992/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040992 none CC1=NC(C#N)=C(N=NCC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 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, 3, 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]
0  hydrogens need rotated
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, 82, 21, 21, 5, 21, 21, 5, 2, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 21, 201, 201, 201, 201, 82, 82, 5, 21, 21, 2, 1, 1, 1, 1, 1, 21] 201
rigid atoms, others: [37, 38, 39, 40, 41, 16, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42])
total number of confs: 472
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: REAL300000040992 none CC1=NC(C#N)=C(N=NCC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 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, 3, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 38, 38, 38, 38, 38, 37, 37, 6, 1, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 38, 38, 38, 38, 6, 6, 1, 1, 1, 21, 21, 21, 21, 21, 21, 1] 201
rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41])
total number of confs: 121
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040992 none CC1=NC(C#N)=C(N=NCC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 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, 3, 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]
0  hydrogens need rotated
201  conformations 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, 2, 2, 10, 38, 38, 38, 38, 38, 126, 201, 201, 201, 201, 201, 201, 201, 201, 201, 38, 1, 2, 2, 2, 9, 10, 38, 38, 38, 201, 201, 201, 201, 201, 201, 38] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 609
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040992 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040992
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040992/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040992
Building REAL300000040993
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040993'
/scratch/stefan/7769621/working/building/REAL300000040993 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040993

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040993/0 /scratch/stefan/7769621/working/building/REAL300000040993 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1129)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1129
`/scratch/stefan/7769621/working/3D/1129' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NC(C)C2=CC(C(=O)[O-])=CC=C2OC(C)C)O1)

`REAL300000040993.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040993.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040993/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040993 none CC1=NC(C#N)=C(N=NC(C)C2=CC(C(=O)[O-])=CC=C2OC(C)C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', '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', '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, 8, 1, 1, 8, 1, 8, 8, 5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 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, 7, 7, 7, 2, 2, 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]
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: [103, 103, 103, 103, 103, 103, 54, 54, 8, 1, 8, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 19, 19, 103, 103, 103, 103, 8, 8, 8, 8, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19] 170
rigid atoms, others: [32, 33, 34, 9, 11, 12, 13, 14, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 215
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040993 none CC1=NC(C#N)=C(N=NC(C)C2=CC(C(=O)[O-])=CC=C2OC(C)C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', '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', '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, 8, 1, 1, 8, 1, 8, 8, 5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 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, 7, 7, 7, 2, 2, 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]
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: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 41, 41, 103, 103, 103, 103, 103, 103, 103, 103, 103, 168, 170, 170, 1, 2, 2, 2, 41, 41, 41, 41, 103, 103, 103, 170, 170, 170, 170, 170, 170, 170] 170
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 356
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040993 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040993
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040993/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040993
Building REAL300000040994
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040994'
/scratch/stefan/7769621/working/building/REAL300000040994 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040994

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040994/0 /scratch/stefan/7769621/working/building/REAL300000040994 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1130)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1130
`/scratch/stefan/7769621/working/3D/1130' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NCC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)O1)

`REAL300000040994.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040994.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040994/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040994 none CC1=NC(C#N)=C(N=NCC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 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, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [107, 107, 107, 107, 107, 107, 67, 67, 9, 3, 2, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 107, 107, 107, 107, 9, 9, 3, 3, 1, 1, 1, 1, 3, 3] 107
rigid atoms, others: [33, 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, 37, 38])
total number of confs: 170
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: REAL300000040994 none CC1=NC(C#N)=C(N=NCC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 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, 2, 2, 7, 7, 7, 7, 3, 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: [80, 80, 80, 80, 80, 80, 35, 35, 5, 1, 1, 1, 1, 1, 1, 3, 3, 1, 2, 3, 3, 3, 3, 1, 1, 80, 80, 80, 80, 5, 5, 1, 1, 3, 3, 3, 3, 1, 1] 107
rigid atoms, others: [32, 37, 38, 9, 10, 11, 12, 13, 14, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36])
total number of confs: 135
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040994 none CC1=NC(C#N)=C(N=NCC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 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, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 46, 80, 80, 58, 80, 107, 107, 80, 80, 107, 107, 107, 107, 80, 80, 1, 2, 2, 2, 45, 46, 80, 80, 107, 107, 107, 107, 80, 80] 107
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 546
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040994 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040994
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040994/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040994
Building REAL300000040995
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040995'
/scratch/stefan/7769621/working/building/REAL300000040995 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040995

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040995/0 /scratch/stefan/7769621/working/building/REAL300000040995 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1131)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1131
`/scratch/stefan/7769621/working/3D/1131' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NCC2=CNC3=CC=C(C(=O)[O-])C=C23)O1)

`REAL300000040995.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040995.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040995/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040995 none CC1=NC(C#N)=C(N=NCC2=CNC3=CC=C(C(=O)[O-])C=C23)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [118, 118, 118, 118, 118, 118, 63, 62, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 118, 118, 118, 118, 9, 9, 1, 1, 1, 1, 1] 118
rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 22, 23, 24, 25, 26, 27])
total number of confs: 190
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040995 none CC1=NC(C#N)=C(N=NCC2=CNC3=CC=C(C(=O)[O-])C=C23)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 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, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 56, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 1, 2, 2, 2, 55, 56, 118, 118, 118, 118, 118] 118
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 272
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040995 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040995
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040995/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040995
Building REAL300000040996
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040996'
/scratch/stefan/7769621/working/building/REAL300000040996 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040996

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040996/0 /scratch/stefan/7769621/working/building/REAL300000040996 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1132)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1132
`/scratch/stefan/7769621/working/3D/1132' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(CN=NC2=C(C#N)N=C(C)O2)=CC(Cl)=C1OC(C)C(=O)[O-])

`REAL300000040996.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040996.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040996/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040996 none COC1=CC(CN=NC2=C(C#N)N=C(C)O2)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.1', 'N.1', 'N.2', 'C.2', 'C.3', 'O.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']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [125, 79, 79, 79, 20, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 79, 185, 201, 201, 201, 201, 125, 125, 125, 79, 20, 19, 2, 2, 2, 79, 201, 201, 201, 201] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 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: 474
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040996 none COC1=CC(CN=NC2=C(C#N)N=C(C)O2)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.1', 'N.1', 'N.2', 'C.2', 'C.3', 'O.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']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 9, 62, 62, 79, 79, 79, 79, 79, 79, 79, 1, 1, 1, 1, 1, 4, 10, 10, 12, 12, 4, 4, 4, 1, 9, 9, 79, 79, 79, 1, 10, 10, 10, 10] 201
rigid atoms, others: [1, 2, 3, 4, 5, 35, 16, 17, 18, 19, 20, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 36, 37, 38, 39])
total number of confs: 170
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040996 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040996
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040996/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040996
Building REAL300000040997
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040997'
/scratch/stefan/7769621/working/building/REAL300000040997 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040997

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040997/0 /scratch/stefan/7769621/working/building/REAL300000040997 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1133)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1133
`/scratch/stefan/7769621/working/3D/1133' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NCC2=CC(C(=O)[O-])=C(Cl)S2)O1)

`REAL300000040997.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040997.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040997/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040997 none CC1=NC(C#N)=C(N=NCC2=CC(C(=O)[O-])=C(Cl)S2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 11, 11, 1, 16, 14, 12, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 77, 76, 8, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 201, 201, 201, 201, 8, 8, 1] 201
rigid atoms, others: [9, 10, 11, 12, 13, 16, 17, 18, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 19, 20, 21, 22, 23, 24])
total number of confs: 295
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040997 none CC1=NC(C#N)=C(N=NCC2=CC(C(=O)[O-])=C(Cl)S2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 11, 11, 1, 16, 14, 12, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 9, 9, 58, 201, 201, 201, 201, 201, 201, 201, 201, 1, 2, 2, 2, 57, 58, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25])
total number of confs: 369
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040997 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040997
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040997/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040997
Building REAL300000040998
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040998'
/scratch/stefan/7769621/working/building/REAL300000040998 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040998

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040998/0 /scratch/stefan/7769621/working/building/REAL300000040998 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1134)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1134
`/scratch/stefan/7769621/working/3D/1134' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NCC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)O1)

`REAL300000040998.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040998.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040998/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040998 none CC1=NC(C#N)=C(N=NCC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 3, 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, 191, 191, 67, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 10, 201, 201, 201, 201, 67, 67, 10, 10, 1, 1, 2, 1] 402
rigid atoms, others: [33, 34, 36, 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, 35])
total number of confs: 415
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: REAL300000040998 none CC1=NC(C#N)=C(N=NCC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 3, 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: [82, 82, 82, 82, 82, 82, 67, 67, 9, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 11, 11, 10, 1, 82, 82, 82, 82, 9, 9, 1, 1, 10, 10, 20, 10] 402
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: 158
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040998 none CC1=NC(C#N)=C(N=NCC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 3, 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, 5, 5, 21, 82, 82, 82, 82, 201, 201, 201, 201, 201, 201, 201, 201, 201, 82, 1, 2, 2, 2, 20, 21, 82, 82, 201, 201, 402, 201] 402
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 718
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040998 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040998
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040998/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040998
Building REAL300000040999
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000040999'
/scratch/stefan/7769621/working/building/REAL300000040999 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000040999

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000040999/0 /scratch/stefan/7769621/working/building/REAL300000040999 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1135)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1135
`/scratch/stefan/7769621/working/3D/1135' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NCC2=CC(C(=O)[O-])=CC=C2N(C)C)O1)

`REAL300000040999.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000040999.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000040999/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040999 none CC1=NC(C#N)=C(N=NCC2=CC(C(=O)[O-])=CC=C2N(C)C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 5, 5, 12, 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, 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
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [102, 102, 102, 102, 102, 102, 58, 57, 8, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 102, 102, 102, 102, 8, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4] 102
rigid atoms, others: [9, 10, 11, 12, 13, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36])
total number of confs: 182
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000040999 none CC1=NC(C#N)=C(N=NCC2=CC(C(=O)[O-])=CC=C2N(C)C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 5, 5, 12, 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, 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
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 45, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 1, 2, 2, 2, 45, 45, 102, 102, 102, 102, 102, 102, 102, 102, 102] 102
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 229
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000040999 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000040999
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000040999/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000040999
Building REAL300000041000
mkdir: created directory `/scratch/stefan/7769621/working/building/REAL300000041000'
/scratch/stefan/7769621/working/building/REAL300000041000 /scratch/stefan/7769621/working /scratch/stefan/7769621
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000041000

mkdir: created directory `0'
/scratch/stefan/7769621/working/building/REAL300000041000/0 /scratch/stefan/7769621/working/building/REAL300000041000 /scratch/stefan/7769621/working /scratch/stefan/7769621
Protomer 0 (index: 1136)
Found valid previously generated 3D confromation in /scratch/stefan/7769621/working/3D/1136
`/scratch/stefan/7769621/working/3D/1136' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C#N)=C(N=NCC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)S2)O1)

`REAL300000041000.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000041000.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769621/working/building/REAL300000041000/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000041000 none CC1=NC(C#N)=C(N=NCC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)S2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 12, 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, 2, 2, 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, 174, 174, 42, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 201, 201, 201, 201, 42, 42, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 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])
total number of confs: 358
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: REAL300000041000 none CC1=NC(C#N)=C(N=NCC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)S2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 12, 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, 2, 2, 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: [103, 103, 103, 103, 103, 103, 61, 61, 9, 1, 1, 1, 1, 1, 1, 7, 7, 2, 2, 7, 7, 7, 7, 1, 103, 103, 103, 103, 9, 9, 1, 1, 7, 7, 7, 7] 201
rigid atoms, others: [9, 10, 11, 12, 13, 14, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35])
total number of confs: 187
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000041000 none CC1=NC(C#N)=C(N=NCC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)S2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 12, 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, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 32, 103, 103, 103, 103, 201, 201, 133, 135, 201, 201, 201, 201, 103, 1, 2, 2, 2, 32, 32, 103, 103, 201, 201, 201, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 713
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769621/working/building/REAL300000041000 /scratch/stefan/7769621/working /scratch/stefan/7769621

Finished preparing REAL300000041000
Recording results
/scratch/stefan/7769621/working /scratch/stefan/7769621
Appending to /scratch/stefan/7769621/finished/xaaaabo.*
0: /scratch/stefan/7769621/working/building/REAL300000041000/0.*
Removing working files in /scratch/stefan/7769621/working/building/REAL300000041000
/scratch/stefan/7769621
Compressing combined databse files
/scratch/stefan/7769621/finished/xaaaabo.db2.gz
/scratch/stefan/7769621/finished/xaaaabo.solv.gz


=======================================================
WARNING: STORE_PROTOMERS not executable or a directory!
All results left in place (/scratch/stefan/7769621/finished)
=======================================================

Finalizing...
removed `/scratch/stefan/7769621/working/3D/1137'
removed directory: `/scratch/stefan/7769621/working/3D'
`/scratch/stefan/7769621/working/protonate' -> `/scratch/stefan/7769621/archive'
`/scratch/stefan/7769621/working/input-smiles.ism' -> `/scratch/stefan/7769621/archive/input-smiles.ism'
rmdir: removing directory, `/scratch/stefan/7769621/working/building'
rmdir: removing directory, `/scratch/stefan/7769621/working'
ls: No match.
ls: No match.